Computers and cells

English: "U.S. Army Photo", from M. ...

English: “U.S. Army Photo”, from M. Weik, “The ENIAC Story” A technician changes a tube. Caption reads “Replacing a bad tube meant checking among ENIAC’s 19,000 possibilities.” Center: Possibly John Holberton (Photo credit: Wikipedia)

(Oops! One day late this week!)

A computer has some similarities to living organisms. Both produce something from, well, not very much. A computer program has data input from various sources, and produces output to various sinks or targets. A living organism takes in nutrients from various sources, and produces branches, leaves, fur, bones, blood and other organs.

Of course there are differences. A computer is much, much simpler than a living being, even single celled organism. A computer in general only has a relatively small number of parts, but the “parts” in a living organism number in the billions. And of course, living organisms reproduce, but that may change in the foreseeable future.

English: The heterolobosean protozoa species A...

English: The heterolobosean protozoa species Acrasis rosea Olive & Stoian. Photographed at the Biology of Fungi Lab, UC Berkeley, California. (Photo credit: Wikipedia)

Some animals are sentient, but I’m not going to discuss that here. Maybe in another post.

A computer has hardware, software and operates on data. The data is either part of the software or read from buffers in the hardware. It stores its calculations in “memory”, which is special hardware with particularly fast access speeds.

English: 1GB SO-DIMM DDR2 memory module

English: 1GB SO-DIMM DDR2 memory module (Photo credit: Wikipedia)

The computer produces results by placing data into buffers in the hardware. This results in things happening in the real world, such as printing a letter or number on paper, or more frequently these days, on some sort of screen. It may also do many other things, such as control the flow of water by moving a valve or other control mechanism.

Computers communicate with other computers, by placing data in an output piece of hardware. The hardware is connected to a distant piece hardware of the same sort which puts the data into a buffer accessible to another computer. This computer may be a specialised computer that merely passes on the data. Such computers are called routers (or modems, or firewalls).

Railway network in Wrocław

Railway network in Wrocław (Photo credit: Wikipedia)

Computers, specialised only in their usage, are found in washing machines, cars, televisions, and we all these days have multi-functional computers in our pockets, our cellphones. It would be hard to find a piece of electronic equipments these days that doesn’t have some sort of computer embedded in it. Very few of these computers are completely isolated – they chatter to one another all the times by various mechanisms.

Internet

Internet (Photo credit: Wikipedia)

(Incidentally, I came across a bizarre example of connectivity of things the other day – a wifi teddy bear. Say you are sitting in the lounge and you want to send a message to your child who is in her bedroom. You pick up your tablet and send a message to a “cloud” web site. This sends a message to your child’s tablet which is in her bedroom with her. The teddy bear, which is connected to the child’s tablet by wifi, growls the message to the child. No doubt scaring her out of her wits.)

So in the current technological world everything is connected to everything else. Much like all the cells in a living being are connected to all the other cells in the organism, directly or indirectly. So how far can we take this analogy, where the organism is the network and the individual cells as the computers. (Caveat emptor – I am not a biology expert, so don’t take what I might say from here on as gospel).

A computer consists of hardware, software, and operates on data. A cell is sort of squishy, so “hardware” can only be a relative term, but a cell does have a relatively small number of organelles, such as mitochondria. The nucleus, which contains most of the genetic material, acts as the control centre of the cell, much as the CPU is the control centre of a computer.

The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression—the nucleus is, therefore, the control center of the cell.

In the cell, the genetic material is in some sense the software of the cell. It contains all the necessary information to create the cell itself or more interestingly the information needed to cause the cell to split into two identical daughter cells. This information is generally encoded in the DNA of the chromosomes.

Information flows between DNA, RNA and protein...

Information flows between DNA, RNA and protein. DNA -> protein is another special transfer, but it is not found in nature. (Photo credit: Wikipedia)

The cell also contains, within the nucleus, an organelle called the nucleolus. This organelle (which is part of the nucleus organelle) seems from my reading to mostly relate to RNA, while the rest of the nucleus mostly relates to DNA, very roughly. RNA and DNA perform a complex dance called protein synthesis in organelles called ribosomes.

Cells produce chemicals, which can be consider analogous to computer outputs and receive chemicals from other cells, and so cells communicate, in a sense, with each other. Since all cells are equal genetically, it follows that a cell’s type, liver, skin, lung or brain neurone is determined by factors in its environment.

The model of an artificial neuron as the activ...

The model of an artificial neuron as the activation function of the linear combination of weighted inputs (Photo credit: Wikipedia)

This only loosely true as each cells is the daughter of another cell and inherits its type, but in the early days of an organism’s life, before organs are formed cells do differentiate. Just as when computers were new, they were all very similar, keyboard, monitor, and beige case.

As the computer-sphere evolved, special types of computer evolved, such as routers and modems, and firewalls. Not to mention phones. Computers became specialised. Similarly cells become differentiated, some going on to become liver cells for example, and others brain cells (neurones).

English: Front side of a Juniper SRX210 servic...

English: Front side of a Juniper SRX210 service gateway Deutsch: Vorderseite eines Juniper SRX210 Service Gateways (Photo credit: Wikipedia)

When an organism is young and a cell divides both cells are the same type, but when the organism is very young there is no differentiation. The DNA in the cell contains the necessary information to determine the cell type and tissues and organs are created in the more complex animals.

This process obviously can’t be random, otherwise cells of the various tissue types would be all mixed up. It seems to me, maybe naively, that while the “program” for creating cells is in the DNA, some factors in the environment convey such information as how old the organism is, and what type of cell needs to be created.

an example of a Program

an example of a Program (Photo credit: Wikipedia)

We know from investigations into fractals that a simple equation can result in the creation of an image that looks very much like a tree or grasses and that small changes to the equation can lead to different tree or grass shapes. It is tempting to think that a similar process takes place in organisms – a general rule is given which results in the right sort of cells being produced in the right places.

The problem with the fractal idea is that it only creates simple shapes. An arm with fingers, skin and so on is beyond the capabilities of a fractal process so far as I know. Fractals don’t stop. Again, so far as I know there’s no way to iteratively create a tree structures with leaves.

So the “software” of the cell, the “program” embedded in the DNA doesn’t appear to be analogous to a simple computer program that draws fractals. Of course that doesn’t mean that we can never describe a simple organism completely in fractal terms, and create analogous distinct individuals.

It seems that a long as the analogy is not pushed too far, computers in a distributed network are reasonably similar to living organisms. Please note I am note referring to the fractal type computer programs, but am talking about the way that computers themselves in a network are somewhat analogous to living organisms. Primitive ones!

Sample oscillator from hexagonal Game of Life.

Sample oscillator from hexagonal Game of Life. (Photo credit: Wikipedia)

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Technolust

I’m going to define technolust or technophilia as the almost uncontrollable urge to snap up the latest or most novel technical gadgets. I succumb to this disease frequently, although I do try to keep it under control. I do! Honestly!

I’ve been vaguely wondering about these selfie sticks, the ones where you stick your cell phone on the end of a pole and trigger it by using a bluetooth connection, so when I saw a bluetooth camera trigger in a local shop, I had to buy it. I had to buy it. I had no choice.

Having got it home and played with it for a bit, I now have to find a use for the darn thing! I don’t particularly like selfies and you can only take so many of them, because essentially they are all the one picture with different backgrounds. You could essentially take one photograph against a “green screen” and chromakey in any background you desire.

My particular area of technolust is things related to or containing computer technology. It’s been with me all my life though I didn’t know it until I came across computer technology at home and at work. I had a Commodore 64 computer at home, and at work I worked on the old huge mainframes, mainly IBM ones. But it really blossomed when I came across mini computers, and the early PCs. I had one of the first portable PCs, like the one in the picture.

English: The IBM Portable PC 5155 model 68

English: The IBM Portable PC 5155 model 68 (Photo credit: Wikipedia)

One mainframe computer I worked on had 256kB of memory and we agonised over how we should divide the address space up between three or four “domains”. Another had a staggering 2MB of memory.

Then at the other end of the scale one PC we had we also upgraded to 2MB of memory, which came on a plugin card which was around 30 – 40 cms long and 10 – 15 cms high. We had to leave the top of the case off to use it!

English: Sun 2/50 1 MB Memory Expansion Board ...

English: Sun 2/50 1 MB Memory Expansion Board P/N 501-1020, with SCSI Controller P/N 501-1045 (Photo credit: Wikipedia)

It’s not always physical things that trigger technolust or technophilia. Before all printers came with network connections they were connected (via a parallel cable usually) to a PC. It could then be shared to others over the network. HP produced a “JetDirect” device which connected the printer to the network either via a cable or a card inserted into the printer itself. I still remember the thrill that I got when I connected over the network to a JetDirect device (which is about the size of a small paperback book) using FTP as if it was a small computer in its own right, which in fact is what the device was.

{| cellspacing="0" style="min-w...

{| cellspacing=”0″ style=”min-width:40em; color:#000; background:#ddd; border:1px solid #bbb; margin:.1em;” class=”layouttemplate” | style=”width:1.2em;height:1.2em;padding:.2em” | 20px |link=|center | style=”font-size:.85em; padding:.2em; vertical-align:middle” |This file was uploaded with Commonist. |} Category:Uploaded with Commonist Deutsch: HP Druckserver Jetdirect 600N mit Ethernet und BNC für den Einbau in Druckern (Photo credit: Wikipedia)

I’ve got altogether too many computer-related devices in the house. Some I use all the time and others are gathering dust. If I was truly obsessive I could fill the house with devices and possibly go broke, but I haven’t gone to those extremes. So I have a “server” and a “workstation”, and my wife has a laptop. Strictly speaking I have a laptop, but I don’t boot it up very often. It is my wife’s old laptop which I fixed and rebuilt.

Some time ago we got an iPad, which I found amazing – something the size of a magazine, which was able to do much of what the other more conventional computers were able to, and which was run by the touch of a finger (or two!). I also got an Android phone and I fell in love with the thing, so I had to have an Android tablet. Had to. No question!

I love my Android tablet! It’s a rare day when I don’t use it two or three times and often it is more than that. I investigated programming for it, though I don’t have a “killer app”, so most of my programming efforts are uncompleted. I mostly use it for reading ebooks, getting the latest news and to a lesser extent for email and other online web browsing.

I also use it for games. When I go to bed I take the tablet with me and complete a couple of Sudoku puzzles or similar before I go to sleep. Experts advise against this, but it works for me.

English: IRex iLiad ebook reader outdoors in s...

English: IRex iLiad ebook reader outdoors in sunlight. Electronic paper. Electrophoretic display. Français : Bouquin électronique iLiad de Irex dehors à la lumière du soleil. Papier électronique. Ecran électrophorétique. (Photo credit: Wikipedia)

Many people these days appear to be afflicted with technophilia or technolust. When a new Apple device is released queues form at the Apple stores worldwide as people try to slake their desire for latest gadget. This is strange as their old devices, which used to be the latest devices at one time, are not rendered useless by the new devices, and transferring personal information to the new device can be challenging, in spite of attempts to make it easy.

English: iPhone 4.

English: iPhone 4. (Photo credit: Wikipedia)

Technolust also extends to software. Some people just have to have the latest apps, the latest operating system. The usual justification for such an upgrade is usually justified by the user as a desire for the new features in the new software or bug fixes in the new software.  While I would not advocate never upgrading software, I find such justifications a little weak.

There is a danger that a software upgrade may “brick” a device, that is, it might stop the device from booting up and being used, which is why many people shy away from upgrades. While this is a real concern such happenings are rare and most upgrades go OK. Nevertheless, most users of technology have a horror story  about how things have turned to custard during an upgrade.

I’m what I would classify as a cautious early adopter. For instance, when the new software was released for my phone and tablet, and these devices informed me that the update was available, I waited for a few weeks and followed the news on the upgrade on the Internet. This is almost always a bad idea as long conversations between people who have had trouble (interspersed with odd rare comment “It went OK for me”) doesn’t encourage one to upgrade!

IPod touch with software upgrade and web clips

IPod touch with software upgrade and web clips (Photo credit: Wikipedia)

Those who grow up with technology tend to use that technology without giving it much thought. Televisions are part of the environment. Cell phones are part of the environment. Maybe soon 3-D printers will be part of the environment. Smart phones and tablets, while desirable, are not quite so novel to the kids of today. They will no doubt direct their technolusts to other technologies.

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Beauty – and the beast

Beauty and the Beast (1992 film)

Beauty and the Beast (1992 film) (Photo credit: Wikipedia)

Modern society has something of a fixation with beauty. This has led to such bizarre things as “boob jobs” or cosmetic breast enhancements. Other women inject toxins like “Botox” into various parts of their anatomy to firm them up.

Whole magazine shelves are devoted to “beauty” magazines, and in recent times, they have been augmented by rows of magazines devoted to exercise. TV “infomercials” extol the virtues of this or that exercise machine for men or women, designed to perform miracles on a person’s shape for as little as 10 minutes exercise per day.

Somewhere there may be someone who is happy with their weight and body shape, but I doubt it. I know that I am not completely happy with mine, but I don’t obsess over it. Some people turn around it and strive in the opposite direction from the mean and try to become, say the heaviest man in the world.

None of this artificiality is beauty. If one measures a beautiful woman for example, one will probably find that the statistics of her measurements are well removed from the average. Miss Beautiful Woman 2015 is way down the bell curve in many ways.

English: Angelina Jolie at the 2010 Comic Con ...

English: Angelina Jolie at the 2010 Comic Con in San Diego (Photo credit: Wikipedia)

Angeline Jolie, considered to be a beautiful woman, says:

I don’t see myself as beautiful, because I can see a lot of flaws. People have really odd opinions. They tell me I’m skinny, as if that’s supposed to make me happy.

If Jolie is not 100% happy with her looks, how can other women, with less of the physical advantages of Jolie be expected to feel happy with their lot? Of course most women are realistic enough to know that not all women can look like Jolie (or would even want to for that matter), but that doesn’t stop them wishing. Similar holds for men. Not everyone can look like me or George Clooney.

English: George Clooney at the Paris premiere ...

English: George Clooney at the Paris premiere of “The Ides of March” Français : George Clooney à l’avant-première parisienne des “Marches du pouvoir” (Photo credit: Wikipedia)

It is evident however, that there is not one standard of beauty (for men or women). Beauty pageants promote one standard of beauty, but films and TV promote another. Beauty is very much in the eye of the beholder. Though it is not usually considered to be a usual measure of beauty, body building is also all about having the best body.

There’s a double standard here, of course. People aspire to be beautiful, and to be highly regarded as such, but if someone goes out of his (or her) way to look at beautiful people, on the Internet, in magazines, all around them, it is rightly considered that there is something wrong with them.

So on the one hand you have people who want to be beautiful, and that is pointless if they are not seen to be beautiful and on the other hand you have people who are obsessed with beauty, which is unhealthy. Of course most people as is usual fall somewhere in the middle ground – they want to be prettier, but they wouldn’t go to the lengths of cosmetic surgery or Botox.

So you have people who go to the gym twice, eat a week and a half of “healthy” food and then relapse back to their usual ways. They then feel some degree of remorse, have some degree of acceptance, and maybe resolve to try again some time in the future. (It’s these people who the gyms make their money out of, not the enthusiasts who turn up week in week out!)

Gym Cardio Theatre Category:Gyms_and_Health_Clubs

Gym Cardio Theatre Category:Gyms_and_Health_Clubs (Photo credit: Wikipedia)

Some expressions of the search for beauty verge on the bizarre. In particular the “child beauty pageants” are disturbing and border on the weird. Very young children are dressed up and made up like adults with revealing costumes and perform suggestive actions and dances on stage. Costumes sometimes include fake breasts on children well under teenage.

I personally find these shows distasteful. It teaches mostly female children pretty much all the wrong things about sexuality. The parents of the children justify these shows by claiming that it gives the child confidence and often that the child is the one that is driven by the urge to compete.

English: A young girl in Mauritania.

English: A young girl in Mauritania. (Photo credit: Wikipedia)

All this happens in a world where parents are told to constantly be on their guard on behalf of their children. The message is that there is a sexual predator behind every bush. While the advice to be on guard for the children is good advice, is it true that there are a vast number of pedophiles out there?

It seems unlikely that there are more than there were in previous generations. It may be that there is more opportunity for such people as people these days know far less about their neighbours than previously and people do move about much more than they used to. Maybe this has allowed such people to. if not flourish, to become more of an issue.

Danger Ahead

Danger Ahead (Photo credit: Wikipedia)

Even so, I think that the pendulum has swung a little too far in the wrong direction. Sure we should keep our children safe, but it seems that parents are being targeted for innocent photographs of their children. It would be a rare parent who has not taken photographs of their children in the bath, and to think that taking such photographs is a sign of a perversion is perverse.

To parents, their children are beautiful, clothed or unclothed and while it not impossible that parents could be sex offenders in that way, it is probably very rare. I’d suggest too, that it should be relatively quick and easy to determine whether or not parents are sex offenders. Here is another article about the case of a family in England, in which the authorities explain some of their thinking in such matters.

My sister and her baby.

My sister and her baby. (Photo credit: Wikipedia)

In one case of beauty and the beast, the beauty and the beast are the same. I refer to the situation where a young lady dresses in a beautiful if revealing dress and proceeds to get very very drunk. There is nothing beautiful in a young lady throwing up into a bush or stumbling into the gutter, not to mention the danger that she is putting herself in by getting into such a state.

Obviously the fact that a drunken woman might be vulnerable does not in any way justify someone taking advantage of her while she is in that state. Nothing does.

 

 

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Lemmings

English: Traffic Jam in Delhi Français : Un em...

English: Traffic Jam in Delhi Français : Un embouteillage à Delhi (Photo credit: Wikipedia)

In Australia there have been traffic jams up to 28 kilometres long. In New Zealand the end of the holiday period is likely to create “traffic hell“. Meanwhile, those of us who have stayed at home, have found the roads to be eerily empty.

Why do people rush away at Christmas in the Southern Hemisphere? Of course, it is our summer, and getting away from home for a few days is always attractive, but it is evident that if thousands of people try to travel the same roads at the same time there will be congestion.

I call those who join the exodus and arrival progressions lemmings. This is of course unfair to both the furry creatures and to the humans. Lemmings don’t really commit mass suicide, and the humans, in many cases, don’t have a lot of choice of travel time.

In the Garfield cartoon, Garfield meets a mouse who is half lemming. Garfield asks the mouse what a lemming is. The mouse replies “A gerbil with suicidal tendencies”. (This cartoon may be online, but I’ve been unable to find it. The Garfield strip for my birthday is quite funny, though.)

In our bigger cities, there will always be traffic problems, because of the sheer number of people that need access to the CBDs and who have to come, in the main from dormitory suburbs. If the roads were sufficient to carry all the traffic it is likely that there would be little room for the CBD itself.

The land of the automobile, the USA, has probably reached the best compromise between the needs of the car and the needs of those who live and work in the centres of cities. Special roads carry cars from the outskirts to the centres of the cities where special buildings have been built to house the cars during the day while the owners are working and shopping. Other special roads take traffic past the city centres and on to other cities. Other countries have copied or extended this model.

Nighttime view of Downtown Los Angeles and the...

Nighttime view of Downtown Los Angeles and the Hollywood Freeway, USA. (Photo credit: Wikipedia)

Humans often don’t have much choice of when they travel, given that they have to work and working days around holidays are pretty much fixed. Some places even shut down on certain days to avoid having to staff offices when few people will be around.

In the Southern Hemisphere Christmas falls in summer, so the natural desire is to go away from home at this time of the year, on a holiday or, as they say in the USA, on a vacation. So it is unfair, really, to call them lemmings. They don’t have a lot of choice.

English: Bank Holiday Monday traffic approachi...

English: Bank Holiday Monday traffic approaching Horncastle This queue stretched from the town centre beyond the speed limit signs. Oh joy! (Photo credit: Wikipedia)

The lemmings are unfairly tagged with the appellation of suicidal maniacs. The story goes that periodically the lemmings migrate usually as the result of population pressures. Geographical features have changed over the millennia and consequently the lemmings fall over cliffs (which didn’t feature in the ancestral environment) or drown in rivers and fjords which have widened since their ancestors swam them.

Illustration of swan-necked flask experiment u...

Illustration of swan-necked flask experiment used by Louis Pasteur to test the hypothesis of spontaneous generation. (Photo credit: Wikipedia)

These theories were used to “explain” why numbers of lemmings are found dead at some times and dead lemmings are rare at other times. The Wikipedia article on the animals has some interesting theories on issue, such as the spontaneous generation of the animals in mid air resulting in their demise on hitting the ground.

While we may laugh at these theories, we must remember that in 1530s science was nowhere nearly as sophisticated as today. In 500 years time, it may be that our scientific knowledge may look just as silly.

I believe that people don’t have to all travel at the same time. Sure the dates are constrained and working requirements also constrain the dates that people can travel, but usually there is some leeway. People could travel a day earlier or a day later. Most employers are more than happy to accommodate such slight variations. If it is impossible for an employee to vary travel dates then a change of travel times would do the trick.

Frequently the call is for the roads to be widened or, as the euphemism has it, improved. This solution may well work in a country like the USA which has a large population which is concentrated in cities with little population in between, but is problematic in smaller countries. In New Zealand, not only are the main centres much smaller, but the population is a lot more dispersed than in the USA.

English: Traffic problems are not new.. Did bo...

English: Traffic problems are not new.. Did both sides have separate car parks? Did Proud Edward go home to think again about the terrible state of London’s traffic congestion. Outside the car/lorry park. A reenactment? (Photo credit: Wikipedia)

When these factors are considered, it may not make sense to continue to continue to build wider highways in smaller countries. A six lane highway that may be heavily used four times a year doesn’t make economic sense. A four lane highway that is heavily used much of the time does make sense.

English: View of Moscow's MKAD / highway ring ...

English: View of Moscow’s MKAD / highway ring Deutsch: Blick auf den Moskauer Autobahnring MKAD (Photo credit: Wikipedia)

I frequently hear people call for “improvement” of roads that I regularly travel with few hold ups and issues. This is because I travel at times which are called “off peak”. People travel to work at the same times every day, and consequently you can travel easily in the opposite direction to the majority and wonder if they could not slightly change their schedules to avoid the hold ups, and indeed some people do do so.

English: Tilehurst Road This is normally chock...

English: Tilehurst Road This is normally chocker with traffic in the morning peak period. After a night of steady snow, on the Friday before Christmas, many people had decided to stay at home. (Photo credit: Wikipedia)

Some people travel in to work very early (and leave early too, of course). Some people “work from home”. This latter can be a euphemism for goofing off of course, but most people who work from home treat this option seriously and with the state that the art of technology has reached, people can usefully contribute from home.

There is an example of the pitfalls of merely “improving” roads near where I live. When I came to this city I recall sitting in traffic on a four lane (two each way) highway into the centre of the city. Subsequently a motorway was built into the city and the four lane highway is relatively lightly used. (The road I refer to is on the left of this picture).

On the right State Highway 1 (SH1) Wellington ...

On the right State Highway 1 (SH1) Wellington motorway, and in the centre the North Island Main Trunk (NIMT) rail lines heading for Porirua and the Wairarapa Line rail lines heading for the Hutt Valley : from left Wairarapa up, NIMT up, NIMT down, Wairarapa down. Wellington, New Zealand. (Photo credit: Wikipedia)

Obviously in this case the motorway was not considered at the time that the four lane highway was built, but it does demonstrate that often the most obvious solution can often be less than efficient over the longer term.

English: Road Works on the A43. The road is re...

English: Road Works on the A43. The road is reduced to one lane for a section and the temporary traffic light has turned red (seen in the distance). Traffic is beginning to emerge from the other direction. (Photo credit: Wikipedia)

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Growing up, down and sideways, and George Clooney.

Ginkgo seedling 1

Ginkgo seedling 1 (Photo credit: Wikipedia)

Often a plant seed will end up in a place that is not particularly suitable for it. In particular it may end up in a gravel path or similar where there is little real soil. Or it may end up in sand which drains quickly and may, if near the sea, contain high amounts of salt.

In such an environment it may grow stunted or may be deformed. For instance Bonsai trees are kept in a small container and kept relative short of nutrients so that stay small and become gnarled and twisted. They may even have their roots trimmed.

Bonsai IMG 6396

Bonsai IMG 6396 (Photo credit: Wikipedia)

One can imagine a society of concerned individuals fighting against the sustained torture of the trees treated in such a manner, but strangely, I’ve never heard of one. Maybe it is because trees can’t scream?

All members of a species have the same genetic make up, the same genotype. All individuals grow in much the same way, to produce similar adult individuals. This is termed the phenotype.

Genetics diagram: Punnett square describing on...

Genetics diagram: Punnett square describing one of Mendel’s crosses, between parents that are heterozygous for the purple/white color alleles. Category:Punnett squares (Photo credit: Wikipedia)

There may be sexual dimorphism, where the female of the species differs from the male of the species, but in most ways, all members of one sex are pretty similar to one another. I am not too dissimilar from George Clooney. My wife is much like Angelina Jolie.

Of course individuals are not identical. I’m slightly taller than George, for instance. This difference can be genetic, or it may be environmental. My genes may be the cause of the difference, or maybe the environment when we were growing up has slightly affected our growth. Our good looks are almost certainly genetic.

English: George Clooney at the Toronto Interna...

English: George Clooney at the Toronto International Film Festival 2011. (Photo credit: Wikipedia)

Sometimes a plant grows in a particular way in one environment will look completely different in another environment. Also a young specimen of a plant may look different from a mature specimen of the same species. Lanceword (Pseudopanax crassifolius) has a juvenile form so different from the mature form that it was initially thought to be two different species.

The environmental effect on the phenotype or expressed shape can be seen in genetically identical twins. One would expect their phenotypes to be identical at all ages, however, while “identical twins” look very very similar there are detectable differences.

English: Comparison of typical zygote developm...

English: Comparison of typical zygote development in monozygotic identical and dizygotic twins. (Photo credit: Wikipedia)

For instance if one twin had suffered a serious illness at a critical stage of growth, then their adult sizes may be significantly different. If one twin had a rich diet and the other twin a restricted diet that also might affect their sizes and expectations of longevity. Scientists can tell a lot about the processes of growth and development by studying genetically identical twins.

A more subtle variation in the phenotype can be seen when populations are considered rather than individuals. A population of moths that lives on darker surfaces may tend to be darker in colour than the same species that lives on lighter surfaces. Since this effect happens slowly, over many generations, it appears to be a genetic change or shift. However this change to the genotype is at a lower level than the species as the lighter moths and the darker ones can interbreed.

A black-bodied peppered moth (Biston betularia...

A black-bodied peppered moth (Biston betularia f. carbonaria) in the Ahlenmoor, a hill moor in northern Lower Saxony, Germany. (Photo credit: Wikipedia)

Some plants look completely different if grown in different environments. The weed that grows in gravel may look completely different from the weed that grows a metre away in a more favourable environment. It’s as if a switch has been thrown which turns on a totally different way of “building” the plant, as it may well be something like that.

If the genome of the organisation is a “program” to “build” the plant, it is perfectly feasible that a lack of resources at an early stage in the plant’s life might well kick in a different path in the developmental process from the path that it would take if resources were abundant.

if (abundant_resources == true)

then build_good_version

else build_poor_version

This is a simple branching process in a computer program, but the process is almost certainly a lot more complex in real life. However the principle is sound, I believe.

English: Capsella bursa-pastoris, Brassicaceae...

English: Capsella bursa-pastoris, Brassicaceae, Shepherd’s Purse, flowers and fuits; Karlsruhe, Germany. The fresh aerial parts of the blooming plant are used in homeopathy as remedy: Capsella bursa-pastoris (Thaspi.) Deutsch: Capsella bursa-pastoris, Brassicaceae, Gewöhnliches Hirtentäschel, Blüten und Früchte; Karlsruhe, Deutschland. Die frischen, oberirdischen Teile der blühenden Pflanzen werden in der Homöopathie als Arzneimittel verwendet: Capsella bursa-pastoris (Thaspi.) (Photo credit: Wikipedia)

A simple iterative process can be used to generate complex shapes that look a lot like real plants. Minor changes to the process can cause significant changes to the end results. Tall thin shapes can morph into shorter bushier ones with a few changes to fixed numbers (constants) in the iterative process.

The phenotype of a plant of a particular species will be similar in all individuals. If an individual has leaves, stem, flowers of a particular sort then the phenotype of an individual in a different (eg poorer) environment, will most likely have similar parts, though some differences will be obvious.

POOR SOIL, DAMAGED BY ACCUMULATED SALT, IS EXA...

POOR SOIL, DAMAGED BY ACCUMULATED SALT, IS EXAMINED BY MEXICAN FARMER, GILBERTO BUITIERREZ BANAGA, NEAR MEXICALI… – NARA – 549083 (Photo credit: Wikipedia)

Maybe the stem into of being long and flexible, it may be a lot shorter and stiffer. Maybe the leaves will be a lot thicker and fleshier in the poor environment plant and may therefore be able to retain water which will be scarcer in the poor environment. Perhaps the flower will be more robust in the harsher environment.

One would expect such variations of phenotype, the poor and the rich, to be implicit in the genome if the wider environment is patchy, with areas of rich soil mixed up with areas where the soil is poor. Otherwise, the ability of the genome to be expressed in multiple ways would likely be bred out of the population, as nature always goes for the simpler rather than the more complex.

English: Edge of a ditch on a gravelly, lime-r...

English: Edge of a ditch on a gravelly, lime-rich soil at eastern Jutland, near the Kattegat. Dansk: Grøftekant på gruset, kalkrig jordbund i Djursland, nær Kattegatkysten. (Photo credit: Wikipedia)

The flexibility of the genome is something that the organism benefits from its whole life. For example there are some fish which live in groups of one male and several females. If the single male is killed by another fish, an octopus or a human being, one of the females will change sex and become male, taking the place of the missing male fish.

I’ll not speculate on how that happens in detail, but it seems that it must be implicit in the genome. The trigger is the absence of the male fish, but how the “genetic program” detects this, I don’t know, but once is does it transforms the largest female into a male, presumably by triggering changes in the genetic organs. That’s bound to be a complex process.

Male and female Gold Molly. Watch the Gonopodi...

Male and female Gold Molly. Watch the Gonopodium of the left fish. Its the male. Left is the female fish. (Photo credit: Wikipedia)

The central idea in this post is that the genome is much like a computer program and that the environmental influences are like the parameters to such a program. This is probably an over simplification in many ways, but by considering it as a program can explain why the same genome can produce such different individuals.

A computer program can be controlled by inputs while it is running, and similarly the environment can shape an organism while it is growing and after it has reached maturity. The idea of organism as computer controlled machine is not new, but I like to bring it out and have another look at it now and again.

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The Solstice Again

The Sun rising over Stonehenge on the morning ...

The Sun rising over Stonehenge on the morning of the summer solstice (21st June 2005). A crowd of between 14,000 and 19,000 people greeted the sun as it rose at 04:58 BST. (Photo credit: Wikipedia)

Today is the summer solstice in the Southern Hemisphere, the time when the sun is furthest south in the sky and hence at its highest. From here on in, the days get shorter as we slide back towards winter.

In the Northern Hemisphere,  it is of course the winter solstice, and those living there can expect the days to lengthen, as they move towards summer. Today is the Northern Hemisphere’s shortest day.

English: Daisy Rock's "solstice gap"...

English: Daisy Rock’s “solstice gap”” This shows the gap in the rock along which the sunset is viewed on the longest day. (Photo credit: Wikipedia)

Seasonal lag means that we can look forward to the warmest months of the year after the solstice, and those unfortunate enough to live in the Northern Hemisphere can look forward to a couple of their coldest months before things start to warm up.

I read somewhere that winter months are the months when people tend to put on weight and this was attributed to the fact that in winter, in the coldest weather people tend to exercise less and eat more. The reduced exercise is attributed to the tendency to stay home in the warm, by the fireside to avoid the often hostile weather.

Brooklyn Museum - Fireside Companion - Platt P...

Brooklyn Museum – Fireside Companion – Platt Powell Ryder – overall (Photo credit: Wikipedia)

And the eating more is because, well, what else is there to do but eat, when you are trapped by the weather. Our ancestors used to use up all the reserves that they had laid up for just this occasion, the hams and preserves, dried fruit and root vegetables and so on.

When the summer solstice happens, the weather is warmer and better, so people can get out an exercise, and, for our ancestors at least, agriculture kept them on the move, and the aim was to replenish the stores for the winter months, hence an emphasis on growing rather than eating. Besides, most crops would not be ready for harvesting.

The winter solstice is one candidate for the start of the year. It marks a definite point in the cycle of the year. It’s after the solstice (a few months after the solstice) that things start growing again. The summer solstice is probably not a good choice as things are humming along then, ploughing and planting, growing and nurturing so it doesn’t really fit as the start of the year.

The spring or vernal equinox falls in March, around the 21st in the Northern Hemisphere. This is also a candidate for the start of the year, but to my mind, it is too late. Winter is tailing off at that time, things are starting to grow and because of the seasonal lag, it’s the start of spring. The year, are I see it, is already under way.

Interestingly our fiscal year ends on 31st March. This is the date used by individuals to account for tax obligations. In many countries using the Gregorian calendar, the fiscal year ends on 31st December and almost aligns with the (winter) solstice based year. Other countries which use other calendars have fiscal years which relate to the local calendar.

As I have said the summer solstice in the Southern Hemisphere falls on 21st December (in most years). It is an astronomical point in time, not a whole day and can happen on 20th December. In the decade from 2010 to 2020 it falls on the 20th on three occasions.

The summer solstice, Christmas Day, and the official 1st January New Year Day all fall within just over a week of each other. There is good reason to suspect historical links between these days, and there is much debate on the actual historical relationship between these events.

It is often said that early Christians adopted the winter solstice in the Northern Hemisphere, to squeeze out or replace a pagan celebration at that time. This may or may not be the case (or it may be partially true), but what is evident is that many cultures outside of the Tropics of Cancer and Capricorn celebrate a festival at around the time of the solstice.

World map with the intertropical zone highligh...

World map with the intertropical zone highlighted in red. (Photo credit: Wikipedia)

Between the two Tropics the sun is overhead twice in a year while the sun reaches a southerly point at the time of the southern solstice (winter in the north and summer in the south) and a northerly point at the time of the northern solstice, the hottest time occurs when the sun is overhead. This divides the year into unequal parts in these latitudes.

The climate of these regions is dependant on local conditions, such as whether or not the region is close to an ocean or is in the middle of a continent, and many tropical areas have wet and dry seasons, typically of unequal extents. One example know to many people outside the tropics is the monsoon season when a regions rainfall may predominantly happen.

On the Arctic and Antarctic circle, at the solstices the sun just grazes the horizon at the summer solstice and the day lasts 24 hours. At the winter solstices the sun just barely reaches the horizon and the night lasts 24 hours. Closer to the poles the number of sunless days or days with the sum always above the horizon increase. At the poles the sun is below the horizon for three months and above it for three months. (I hope this is correct. I did research this a little, but I am not 100% sure).

Interestingly, I learnt recently that the sunset will continue to become later for the next few weeks. The reason for this according to the linked article is because we have tied our clocks to 24 hours exactly and the day is not exactly 24 hours long. Not only is it not exactly 24 hours, but its length varies during the year. In Wellington the sunset goes out to around 3 minutes to 9 and doesn’t dip below that time until 7th January 2015.

English: Sunrise at Winter Solstice (December ...

English: Sunrise at Winter Solstice (December 21, 2006 at 8 a.m.) as viewed through the doorway half way up Maiden Tower (Photo credit: Wikipedia)

(December data here, January data here).

While looking up these numbers I noticed that the day length in Auckland is nearly half an hour shorter up there. Also sunset is about a quarter of an hour later in Wellington meaning that when the summer weather finally arrives we will have an extra 14 minutes to enjoy the balmy evenings. That’s yet another reason to prefer Wellington over Auckland! We have more time to celebrate the solstice.

English: Wellington Harbour (New Zealand) view

English: Wellington Harbour (New Zealand) view (Photo credit: Wikipedia)

[Darn! I completed this on Monday but forgot to publish it. Better late than never, I guess!]

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Why Pi?

Based on Image:P math.png

Based on Image:P math.png (Photo credit: Wikipedia)

If you measure the ratio of the circumference to the diameter of any circular object you get the number Pi (π). Everyone who has done any maths or physics at all knows this. Some people who have gone on to do more maths knows that Pi is an irrational number, which is, looked at one way, merely the category into which Pi falls.

There are other irrational numbers, for example the square root of the number 2, which are almost as well known as Pi, and others, such as the number e or Euler’s number, which are less well known.

Illustration of the Exponential function

Illustration of the Exponential function (Photo credit: Wikipedia)

Anyone who has travelled further along the mathematical road will be aware that there is more to Pi than mere circles and that there are many fascinating things about this number to keep amateur and professional mathematicians interested for a long time.

Pi has been known for millennia, and this has given rise to many rules of thumb and approximation for the use of the number in all sorts of calculations. For instance, I once read that the ratio of the height to base length of the pyramids is pretty much a ratio of Pi. The reason why this is so leads to many theories and a great deal of discussion, some of which are thoughtful and measured and others very much more dubious.

Menkaure's Pyramid

Menkaure’s Pyramid (Photo credit: Wikipedia)

Ancient and not so ancient civilisations have produced mathematicians who have directly or indirectly interacted with the number Pi. One example of this is the attempts over the centuries to “square the circle“. Briefly squaring the circle means creating a square with the same area as the circle by using the usual geometric construction methods and tools – compass and straight edge.

This has been proved to be impossible, as the above reference mentions. The attempts to “trisect the angle” and “double the cube” also failed and for very similar reasons. It has been proved that all three constructions are impossible.

English: Drawing of an square inscribed in a c...

English: Drawing of an square inscribed in a circle showing animated strightedge and compass Italiano: Disegno di un quadrato inscritto in una circonferenza, con animazione di riga e compasso (Photo credit: Wikipedia)

Well, actually they are not possible in a finite number of steps, but it is “possible” in a sense for these objectives to be achieved in an infinite number of steps. This is a pointer to irrational numbers being involved. Operations which involve rational numbers finish in a finite time or a finite number of steps. (OK, I’m not entirely sure about this one – any corrections will be welcomed).

OK, so that tells us something about Pi and irrational numbers, but my title says “Why Pi?”, and my question is not about the character of Pi as an irrational number, but as the basic number of circular geometry. If you google the phrase “Why Pi?”, you will get about a quarter of a million hits.

Animation of the act of unrolling a circle's c...

Animation of the act of unrolling a circle’s circumference, illustrating the ratio π. (Photo credit: Wikipedia)

Most of these (I’ve only looked at a few!) seem to be discussions of the mathematics of Pi, not the philosophy of Pi, which I think that the question implies. So I searched for articles on the Philosophy of Pi.

Hmm, not much there on the actual philosophy of Pi, but heaps on the philosophy of the film “Life of Pi“. What I’m interested in is not the fact that Pi is irrational or that somewhere in its length is encoded my birthday and the US Declaration of Independence (not to mention copies of the US Declaration of Independence with various spelling and grammatical mistakes).

Pi constant

Pi constant (Photo credit: Wikipedia)

What I’m interested in is why this particular irrational number is the ratio between the circumference and the diameter. Why 3.1415….? Why not 3.1416….?

Part the answer may lie in a relation called “Euler’s Identity“.

e^{i \pi} + 1 = 0

This relates two irrational numbers, ‘e’ and ‘π’ in an elegantly simple equation. As in the XKCD link, any mathematician who comes across this equation can’t help but be gob-smacked by it.

The mathematical symbols and operation in this equation make it the most concise expression of mathematics that we know of. It is considered an example of mathematical beauty.

The interesting thing about Pi is that it was an experimental value in the first place. Ancient geometers were not interested much in theory, but they measured round things. They lived purely in the physical world and their maths was utilitarian. They were measuring the world.

However they discovered something that has deep mathematical significance, or to put it another way is intimately involved in some beautiful deep mathematics.

English: Bubble-Universe's-graphic-visualby pa...

English: Bubble-Universe’s-graphic-visualby paul b. toman (Photo credit: Wikipedia)

This argues for a deep and fundamental relationship between mathematics and physics. Mathematics describes physics and the physical universe has a certain shape, for want of a better word. If Pi had a different value, that would imply that the universe had a different shape.

In our universe one could consider that Euler’s Relation describes the shape of the universe at least in part. Possibly a major part of the shape of the universe is encoded in it. It doesn’t seem however to encode the quantum universe at least directly.

English: Acrylic paint on canvas. Theme quantu...

English: Acrylic paint on canvas. Theme quantum physics. Français : Peinture acrylique sur toile. Thématique physique quantique. (Photo credit: Wikipedia)

I haven’t been trained in Quantum Physics so I can only go on the little that I know about the subject and I don’t know if there is any similar relationship that determines the “shape” of Quantum Physics as Euler’s Relation does for at least some aspects of Newtonian physics.

Maybe the closest relationship that I can think of is the Heisenberg Uncertainty Principle. Roughly speaking, (sorry physicists!) it states that for certain pairs of physical variables there is a physical limit to the accuracy with which they can be known. More specifically the product of the standard deviations of the two variables is greater than Plank’s constant divided by two.

English: A GIF animation about the summary of ...

English: A GIF animation about the summary of quantum mechanics. Schrödinger equation, the potential of a “particle in a box”, uncertainty principle and double slit experiment. (Photo credit: Wikipedia)

In other words, if we accurately know the position of something, we only have a vague notion of its momentum. If we accurately know its velocity we only have a vague idea of its position. This “vagueness” is quantified by the Uncertainty Principle. It shows exactly how fuzzy Quantum Physics.

The mathematical discipline of statistics underlay the Uncertainty Principle. In a sense the Principle defines Quantum Physics as a statistically based discipline and the “shape” of statistics determines or describes the science. At least, that is my guess and suggestion.

To return to my original question, “why Pi?”. For that matter, “why statistics?”. My answer is a guess and a suggestion as above. The answer is that it is because that is the shape of the universe. The Universe has statistical elements and shape elements and possibly other elements and the maths describe the shapes and the shapes determine the maths.

This is rather circular I know, but one can conceive of Universes where the maths is different and so is the physics and of course the physics matches the maths and vice versa. We can only guess what a universe would be like where Pi is a different irrational number (or even, bizarrely a rational number) and where the fuzziness of the universe at small scales is less or more or physically related values are related in more complicated ways.

The reason for “Why Pi” then comes down the anthropological answer, “Because we measure it that way”. Our Universe just happens to have that shape. If it had another shape we would either measure it differently, or we wouldn’t exist.

 

 

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