Cell biology – Me on the net

Philosophy and Science



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Philosophy can be described, not altogether accurately, as the things that science can’t address. With the modern urge to compartmentalise things, we designate some problems as philosophy and science, and conveniently ignore the fuzzy boundary between the two disciplines.

The ancient Greek philosophers didn’t appear to distinguish much between philosophy and science as such, and the term “Natural Philosophy” described the whole field before the advent of science. The Scientific Revolution of Newton, Leibniz and the rest had the effect of splitting natural philosophy into science and philosophy.

Science is (theoretically at least) build on observations. You can’t seriously believe a theory that contradicts the facts, although there is a get-out clause. You can believe such a theory if you have an explanation as to why it doesn’t fit the facts, which amounts to having an extended theory that includes a bit that contains the explanation for the discrepancy.

Philosophy however, is intended to go beyond the facts. Way beyond the facts. Philosophy asks question for example about the scientific method and why it works, and why it works so well. It asks why things are the way they are and other so called “deep” questions.



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One of the questions that Greek philosopher/scientists considered was what everything is made of. Some of them thought that it was made up four elements and some people still do. Democritus had a theory that everything was made up of small indivisible particles, and this atomic theory is a very good explanation of the way things work at a chemical level.

Democritus and his fellow philosopher/scientists had, it is true, some evidence to go and to be fair so did those who preferred the four elements theory, but the idea was more philosophical in nature rather than scientific, I feel. While it was evident that while many substances could be broken down into their components by chemical method, some could not.

Antoine Lavoisier developed the theory of comb... — Antoine Lavoisier developed the theory of combustion as a chemical reaction with oxygen (Photo credit: Wikipedia)

So Democritus would have looked at a lump of sulphur, for example, and considered it to be made up of many atoms of sulphur. The competing theory of the four elements however can’t easily explain the irreducible nature of sulphur.

My point here is that while these theories explained some of the properties of matter, the early philosopher/scientists were not too interested in experimentation, so these theories remained philosophical theories. It was not until the Scientific Revolution arrived that these theories were actually tested, albeit indirectly and the science of chemistry took off.

Model for the Three Superior Planets and Venus... — Model for the Three Superior Planets and Venus from Georg von Peuerbach, Theoricae novae planetarum. Image enhanced for legibility. The abbreviations in the center of the diagram read: C[entrum] æquantis (Center of the equant) C[entrum] deferentis (Center of the deferent) C[entrum] mundi (Center of the world) (Photo credit: Wikipedia)

Before that, chemical knowledge was very run by recipes and instructions. Once scientists realised the implications of atomic theory, they could predict chemical reactions and even weigh atoms, or at least assign masses to atoms, and atomic theory moved from philosophy to science.

That’s not such a big change as you might think. Philosophy says “I’ve got some vague ideas about atoms”. Science says “Based on observations, your theory seems good and I can express your vague ideas more concretely in these equations. Things behave as if real atoms exist and that they behave that way”. Science cannot say that things really are that way, or that atoms really exist as such.

Indeed, when scientists took a closer look at these atom things they found some issues. For instance the (relative) masses of the atoms are mostly pretty close to integers. Hydrogen’s mass is about 1, Helium’s is about 4, and Lithium’s is about 7. So far so tidy. But Chlorine’s mass is measured as not being far from 35.5.

This can be resolved if atoms contain constituent particles which cannot be added or removed by chemical reactions. A Chlorine atom behaves as if it were made up of 17 positive particles and 18 or 19 uncharged particles of more or less the same mass. If you measure the average mass of a bunch of Chlorine atoms, it will come out at 35.5 (ish). Problem solved.

English: Chlorine gas (Photo credit: Wikipedia)

Except that it has not been solved. Democritus’s atoms (it means “indivisibles”) are made up of something else. The philosophical problem is still there. If atoms are not indivisible, what are their component particles made of? The current answer seems to be that they are made of little twists of energy and probability. I wouldn’t put money on that being the absolute last word on it though. Some people think that they are made up of vibrating strings.

All through history philosophy has been raising issues without any regard for whether or not the issues can be solved, or even put to the test. Science has been taking issues at the edges of philosophy and bringing some light to them. Philosophy has been taking issues at the edge of science and conjecturing on them. Often such conjectures are taken back by science and moulded into theory again. Very often the philosophers who conjecture are the scientists who theorise, as in famous scientists like Einstein, Schroedinger and Hawking.

The end result is that the realm of philosophy is reduced somewhat in some places and the realm of science is expanded to cover those areas. But the expansion of science suggests new areas for philosophy. To explain some of the features of quantum mechanics some people suggest that there are many “worlds” or universes rather than just the one familiar to us.

This is really in the realm of philosophy as it is, as yet, unsupported by any evidence (that I know of, anyway). There are philosophers/scientists on both sides of the argument so the issue is nowhere near settled and the “many worlds interpretation” of quantum mechanics is only one of many interpretations. The problem is that quantum mechanics is not intuitively understandable.

The “many worlds interpretation” at least so far the Wikipedia article goes, views reality as a many branched tree. This seems unlikely as probabilities are rarely as binary as a branched tree. Probability is a continuum, like space or time, and it is likely that any event is represented on a dimension of space, time, and probability.

I don’t know if such a possibility makes sense in terms of the equations, so that means that I am practising philosophy and not science! Nevertheless, I like the idea.

10 fingers and 10 toes

[Ooops! Late again.]

The seed pod of milkweed (Asclepias syriaca) (Photo credit: Wikipedia)

Most living things come from seeds or eggs. A fertilized egg or seeds has all the information in it to generate the organism that springs from it. All the organs of the organism are implicit in the egg or seed, but minor details, like freckles or fingerprints are not encoded in the egg.

The environment and chance play a part in the final shape of an organism. A seed may fall in a good environment or it may fall in a less favourable environment and the shape of the organism can be totally different in the two environments, to the extent that an unwary botanist may categorise them as two different species.

This property of plants was used by the writer of the Christian gospel in the Parable of the Sower (Matthew 13:3-23). Interestingly this comes just before the part where the Gospel writer expounds on Jesus’ reasons for teaching in parables.

Some plants and animals change significantly as they mature. Lancewood is so different as a mature plant from its juvenile form. The juvenile leaves are narrow and spiky while the mature leaves are broader and softer, and while there are competing theories as to why this is, my favourite theory is that the juvenile plants had to discourage browsing by animals, and in particular the extinct bird called the Moa. Since the Moa is extinct this theory cannot be tested!

Japanese horticulturists have used this feature of organisms to fit themselves to the environment to create miniature trees in a pot. Basically the tree is grown in a small container which obviously can’t maintain a full sized tree and as a result a perfectly formed miniature tree can be formed with care, sometimes over long periods of time.

It would seem obvious that you can’t produce bonzai human beings, but in fact this can be done. Whenever a drought or famine hits a country the children who grow up there are small and underdeveloped (as well as having other deficiency problems.

When researching this topic I came across an article on the Internet which discusses this topic, and the authors state in part:

Therefore, by coding for proteins, genes determine two important facets of biological structure and function. However, genes cannot dictate the structure of an organism by themselves. The other crucial component in the formula is the environment.

This overstates the role of the environment a little, I feel, as in most cases the organism’s structure is determined in the most part in its genes, so that it looks much like any other member of the species. It is only when the environment is unfavourable (as in the case of the bonzai trees) that the gene expression leads to significantly differently formed individual. Droughts and poor soils will also leads to significantly differently formed individuals, but those are deficiency effects.

Early succession on poor, sandy soil at Øer, D... — Early succession on poor, sandy soil at Øer, Djursland, Denmark. (Photo credit: Wikipedia)

This is more clearly true in the case of organisms like humans. Unless the environment in which a human grows up is very extreme, there is actually little difference between individuals, and those differences, race, eye colour, hair colour and things like the tendency to myopia are almost certainly genetic.

So I am arguing that genes result in the major characteristics of any organism, except in certain rare cases. Somewhere in the human genome the number of fingers and toes are coded for, and only rare individuals with genetic variations have more or less digits. We don’t all speak the same language, but that is not a genetic trait, though the ability to learn and speak a language may be genetic.

Genes are interesting things. As mentioned in the article, genes can code for structural proteins or for enzymes which affect the chemical reactions in the cell. I suspect that the line between the two is pretty blurred as building the structure of the cell is after all a chemical reaction.

Of course, not only must a cell’s genetic mechanism build and maintain its own organisation, but a cell is part of a tissue, and in, for example, the liver, a cell must maintain itself as a liver cell. Similarly for cells in other organs.



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It appears that, as the genetic material is identical across the whole organism, that there must be some way for a cell to “know” that it should develop as liver cell and not as a brain cell. This is done by switching genes on and off, but I don’t understand how this happens in multi-cellular organisms. It seems that there are environmental influences within the organism and within the tissues that determine this.

It’s likely that these environmental influences are based on something like chemical gradients. Otherwise, when a bone is created there would be no way of telling the process of bone creation when to stop. It is evident that it is an approximate influence because fruit flies have different numbers of eye cells between left and right eyes (about 1000). If it were an accurate influence then the number of eye cells would be the same in both eyes.



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Apparently scientists do not know exactly how it work either. In this web page, “10 Questions Still Baffling Scientists“, the claim is made that not even the experts know. Of course these Internet lists of things may or may not be accurate, but it is an interesting link.

Of course fractal generation programs can be used to generate pretty good imitations of the structures of trees, and changing a few parameters fed to the fractal generation programs can change the shape of the “tree” from a bushy structure to an extended poplar type structure.

Some similar mechanism might be involved here. Fractal programs are simple, can produce a wide range of shapes. The trouble with fractals is that there is usually no way to stop the shape generation, so any stopping mechanism is probably not part of any possible fractal method for generating. Some other method for stopping the growth of an organ once it is the right size and shape most likely exists.

From the link above it is possible that this mechanism is not yet known, but it does appear that organ growth and shape is encoded in the genes, and is effected by switching genes on and off. Some fractal type mechanism might be involved.

English: Apprentice. Man and boy making shoes. (Photo credit: Wikipedia)

Computers and cells

(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.

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.

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).

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.

(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).



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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.

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).

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 (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.



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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. (Photo credit: Wikipedia)

Why does cancer spread?

The Human Body -- Cancer — The Human Body — Cancer (Photo credit: n0cturbulous)

Everyone, I’m sure, knows of someone who has died of cancer. It’s a disease that is wide-spread and seems to be more common now that other diseases are coming under control. It may be that cancer is certain to appear in the human body if it lives long enough. There’s a cheery thought.

Wikipedia describes cancer as follows: “known medically as a malignant neoplasm, (it) is a broad group of diseases involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumours, and invade nearby parts of the body”.

There’s two parts of this definition. Firstly there is the unregulated cell growth and secondly there is the spread of the growth to other parts of the body. The unregulated cell growth is usually attributed to a number of causes, but the mechanism is usually given as damage to the genetic material. The causative agent whatever it might be, damages the genetic material and this results in a huge proliferation of cells.

I write computer programs as tools for doing my job. Each program ends up as a string of data which a human has a hard time decoding, though of course the computer hardware has no problems. The effect of changing a single bit (actually, a byte) of a program would almost certainly cause it to crash. In so far as the analogy that the genetic code resembles a computer program holds, this indicates that a random change to the genetic code would most likely result in the death of the cell. It would require a specific hit, to say a piece of code that control the termination of a loop that would let the program “grow out of control”.

Out of memory ATM (Photo credit: RuiPereira)

I’d guess, from a position of almost total ignorance, that changes to the cells in the body occur all the time. Changes happen to the genetic code in a cell, and it almost certainly dies. (A side question is : what exactly happens to a cell when it dies? Presumably some process or other ‘detects’ the death and breaks it up? Or does the first failure cause other processes to fail until the integrity of the cell is lost? Lots of questions). However, unless the failure is dramatic, explosion-like rather than simple deflation, it should not affect its neighbouring cells, should it? So in general the death of a single cell is probably not noticeable.

Going back to the computer program analogy, in a computer there are dozens, if not hundreds of programs running all the time, but the user is not aware of any other than the one he is interacting with. Equating cells with computer programs, it is most likely that a random change would cause a program or a cell to die, with little effect on the computer or body as a whole.

Facit computer memory (Photo credit: liftarn)

All the programs running in a computer need ‘memory’ to run in, and there is a limited supply of memory, so (conceptually at least) one program is given the task of managing the memory allocations. Damaging the memory manager program could theoretically lead to it repeatedly allocating memory until there was none free for allocation. The computer would, once again, crash. If a program is damaged in a particular way it could ask repeatedly for memory and again cause itself or other programs. or even the whole computer to crash.

In a living organism there does not seem to be a single equivalent of the ‘memory manager’ or ‘resource manager’. In a living organism everything seems to be done by consensus between cells. (That is both anthropomorphic and probably naive, but it will do, I think).

So, although I’d estimate that the vast majority of changes to the genetic code would result in cell death and nothing else, a very, very small number of changes could result in the cell soaking up as much of the cell-level resources as it can and damaging the cell itself, its neighbouring cells or the whole organism.

That, however, is not cancer. For damage to result in a cancer it has to damage the cell in a particular way. In a computer, cancer would be analogous to a program continually creating copies of itself and using up all the system resources, which would result in the system crashing. Almost all cells have the ability to duplicate themselves, but whether or not they do replicate is, so far as I know, determined by the conditions in the cell itself and conditions in its environment, ie the surrounding cells, possibly signalled by chemicals or chemical gradients.

For a cell to become cancerous, it first of all must be inclined to duplicate itself and it would also have to be able to ignore any signals from its environment. The damage to the genetic structure to achieve this seems to me to be remarkably specific. Its like damaging a computer program in such a way as to destroy a control loop. Possible, but not very likely.

Then there is the issue of metastasis. This is how cancer spreads. It first of all attacks the boundary of the organ it is embedded in, then some cancer cells migrate into other organs. Interestingly, when they start to form a cancerous tumour in the new organ, they are still identifiable as cells from the original organ.

Think for a moment about what that means. A cancer which metastasizes has to have its genetic material damaged in such a way that it can do all of the following :

divide in an uncontrolled manner
attack the walls of the organ it is contained in
migrate to other organs (and it can be very specific about the organs it migrates to)
settle there and start to divide again

That’s a remarkably specific set of actions to occur as the result of damage. Damage usually results in less efficient operation, both of computer programs and bodies. Of course the damage doesn’t have to create these action ‘programs’ in the genetic material. They may be already there. All that the damage needs to do is somehow kick off those actions in sequence to cause the cancer to form and metastasize. To a programmer it would look like a small chunk of code to call those routines which I’ve called ‘actions’. The only other time in one’s life that one’s body experiences explosive growth and cell migration is in the womb and as a young child. One can imagine that damage could somehow kick off the genes or part of the genetic code that was used when one was a developing foetus.

This is easier to contemplate than damage which somehow creates the whole process from scratch. It does imply that the damaging agent somehow attacks a specific part of the genetic material and replaces it with some very specific other material that has the specific effect of kicking off explosive growth and metastasis.

I’m not geneticist or cancer specialist of course, so my musings above may be way, way off beam. They could be and probably are complete rubbish. I can’t and won’t defend them if anyone were to attack them. My main thesis is that it seems incredibly unlikely that damage to the genetic material could cause the specific effects of cancer, which are uncontrolled growth and metastasis.

Yet cancer happens and happens frequently and in varied ways. There are many sorts of cancer and they appear to be often triggered by specific stimuli. All my arguments above founder on that logical rock.