Genetics: Does DNA also encode mathematical values of lengths, distances and angles ?

Hi all,

Ok, it's time to delve into biology, genetics and human anatomy ... may even throw some evolutionary theory into the mix as well ... and see what surfaces !

I've been casually interested in the biological sciences since high school and have for most of the years since then taken it on faith that genetics has become a successful and proven theory explaining the development of virtually all life forms on Earth over the many millenia.

Before I get into the main topic of this thread, a little bit of genetic refresher may prove useful to some readers.


We're taught that all species have their own specialized central repository and data bank, known as DNA (deoxyribonucleic acid), that contains the genetic blueprints, instructions and characteristics necessary for the complete physical creation of that specie.

DNA is a specialized and very long chain molecule that has evolved to fulfill two main goals. One being to efficiently and effectively store genetic information within it's chemical and molecular structure.
As well, as storing all the information required to construct a given specie, it also has under the right conditions, the unique property of being able to replicate itself with virtually no errors. Thats not to say that errors don't occur, which they do from time to time (mutations), but that the replication process is on the whole incredibly effective.

As most people are probably aware by now, DNA is a unique molecule that has the shape of a double helix.
Here's an example of it's shape ...

[atsimg]http://files.abovetopsecret.com/images/member/68cb8a9eaeae.jpg[/atsimg]


Now, whenever a cell divides, the original genetic information is completely reproduced resulting in each and every cell receiving it's own copy of the entire DNA base. There are some cells e.g. sperm, etc that don't receive a full copy but that's not pertinent to this thread's topic.

So let's start of with a single human cell resulting from sperm/egg fertilization.

Shortly afterwards, the cell divides, then soon afterwards these 2 cells in turn divide ... then the 4 cells divide and so on and so on.

Ok, so we're at the point where cells are dividing, each getting a full copy of the genetic database and soon will start to specialize and turn into certain cells e.g. heart cells, skin cells, brain cells, etc, etc ... all based upon the genetic instructions contained within the DNA.

Before not to much time has passed, the developing foetus begins to show recognizable developing body parts such as arms, legs, head, etc. The biochemistry of these cells I don't really have a problem with as the necessary internal components of the cells are constructed from the information encoded within the DNA ... and each cell has access to this information.

But now comes the point at which I have to admit that a certain level of confusion begins to set in.
Each organism eventually has a certain physical shape and in humans, this is inevitably 2 arms, 2 legs, a head, 2 ears, 2 eyes, hands, fingers, etc. Now these are obviously the external shape and appearance of the organism. But there are also internal 3 dimensional structures e.g. blood vessels, the brain, the heart, the liver, kidneys, stomach, etc, etc.
So where is the information stored that determines the "physical" 3 dimensional shape (internal and external) of the organism ? Presumably also somewhere within the DNA
How is this information retrieved and used ?


Let me try and make my point a little clearer ...

As the foetus begins to grow and develop a physical shape, we see as an example the beginning of what will eventually say, become an arm ... complete with bones, blood vessels, skin, wrist, fingers, nails, etc.
Initially this arm starts to develop from just a few cells located on a specific part of the foetuses body. Now for a fully functional and complete arm to be created, cells will need to divide and begin to extend away from the main body out into the surrounding space.
The completed arm will have a physical shape thats recognizable as an arm which means that during the entire process of creating the arm, millions of cells will become involved and will require knowledge of their position in space and their position relative to all the other cells busily working away at creating their part of the arm. Otherwise if cells were allowed to simply divide and position themselves randomly, the foetus would most likely end up with a blob or some other weird shape for an arm.
The fact that an arm most times develops in the right place and looks like an arm, must mean that every cell that played a part in the construction of that arm must have also been supplied or had access to spatial positioning information and some kind of coordination system ... information that would say "get x number of cells to divide but only in THIS direction only and then stop ... then get y number of cells to divide but only in THIS different direction, then stop."
The end result being millions and millions of cells that were busily involved in doing their own little local bit and unable to see any other cells except their immediate neighbours, yet alone the large picture ... and yet still managing to coordinate their individual activities to create a perfect 3 dimensional shape (arm) that was just so long and just so wide and had just the right amount of fingers separated from each other by just the optimal angles.

A similar example can also be had by looking at blood vessels. There are estimated to be many kilometres of blood vessels comprising arteries, veins and capillaries in the human body ... and yet these blood vessels are able to grow in the correct physical direction for the correct physical distance ... stopping when required and allowing another vessel to branch of in a completely different direction for a completely different distance and still managing to successfully connect with another blood vessel on the opposite side of the body.

Again, where does all the required physical length, distance, quantity, time information come from ? how is it stored and retrieved ? how does the bone or blood vessel know that its grown long enough in a certain direction and distance ? how does the vessel or bone know that it needs to continue growing but in a different direction and distance ?

Continued next post ...

Continued from previous post ...


And how could all those millions of heart cells succesfully cooordinate together to create the 3D shaped heart in billions of humans without guiding information to determine where each and every heart cell needs to be to result in that recognizably shaped structure ? The fact that every foetus can grow an essentially identical heart structure means there has to be spatial/physical template information stored and available, somewhere.

So, eventually we end up with a fully grown and developed human comprised of cells built from instructions contained within the DNA.

But this is not just a formless, shapeless mass of billions of cells resulting from the billions of randomly occurring cell divisions ... these billions of cells have an overall 3D physical and spatial design which could ONLY be the result of physical properties of distance, length, angle and time being stored somewhere and subsequently accessed somehow by each and every cell so that it was in the correct position, at the correct angle, for the correct distance and for the correct length, and at the correct moment in time.

I have never come across any references to spatial positioning or physical construction template information being encoded into DNA even though geneticists have admitted that there appears to be a substantial quantity of what they call "junk" DNA that apparently serves no useful function and could be discarded remnants of our evolutionary past.

So, could this spatial template information actually be stored within the DNA along with the construction instructions for each type of cell ... or is it obtained from somewhere external to the organism itself ?

If it's stored in the DNA itself, then how are angles, lengths and distances encoded ? How are they retrieved and used ?

If it's stored and obtained externally to the DNA, then that's a whole new topic for discussion !

Irrespective, I can't believe for one moment that there is NOT some kind of overall controlling template/mechanism that makes one specie look like a human and another specie look like a horse ... each and every time.

Has anyone come across information that either substantiates or refutes any of the above ?

Hmmm ... you raise a very interesting point.
Now that I stop to think about it, there must be some validity in your ponderings regarding some kind of inherent controlling influence on the physical shape of our organs. Something must prevent our dividing cells from just placing themselves randomly and instead direct them into a resultant and specific 3d shape.
And by extension, this implies as you said, a knowledge of distance, angles and lengths must be somehow available.

Certainly food for thought !

S&F

I think that what happens is the DNA triggers off chemical processes that result in growth. As the fetus grows (the cells divide), there may be some "counter" that says how many divisions of what types of cells are needed. After a certain number of repetitions, the next phase is begun, with a new "counter".

Since these chemical processes take a certain amount of time each, having a counter is similar to instructing the cells to do something for a certain amount of time - so at X number of weeks, the fetus has these features, and at Y weeks it has others, more complicated and more human-like.

I don't think that there is any information about angles and lengths directly into the DNA, but rather just instructions about how long (or how many times) to proceed in each phase.

I agree, thats a very novel concept you've just raised.

I know that a sequence of nucleotides (a gene) stores information that can be eventually "read" and transcribed into a protein that does some kind of "useful" work within the cell, but how the heck would mathematical values be stored using a nucleotide sequence and how would those values be "read" when required ?

Mind you, I'm NOT disagreeing with you as I also accept that there MUST be a controlling template/values that for example instruct a blood vessel to be exactly say, 5 cms long before it branches away at a 35 degree angle so that it can join up successfully with another blood vessel 3 cms away. Having the blood vessel just grow in a random direction for a random distance just won't work.

Originally posted by chiron613
I think that what happens is the DNA triggers off chemical processes that result in growth. As the fetus grows (the cells divide), there may be some "counter" that says how many divisions of what types of cells are needed. After a certain number of repetitions, the next phase is begun, with a new "counter".

Since these chemical processes take a certain amount of time each, having a counter is similar to instructing the cells to do something for a certain amount of time - so at X number of weeks, the fetus has these features, and at Y weeks it has others, more complicated and more human-like.

I don't think that there is any information about angles and lengths directly into the DNA, but rather just instructions about how long (or how many times) to proceed in each phase.

I agree that there must be certain chemical control processes that instruct a cell how many times to divide ... but surely without some form of input instructing the cell as to which direction the resulting divisions should go, you'd end up with nothing more than a mass or blob of cells with the original cell stuck in the centre of the mass.

Take the femoral artery as an example:
it's approximately 4 cm in length and divides into superficial femoral & profunda femoris arteries.

What instructs the femoral artery at each branch point which direction to take with further cell divisions so that it successfully locates and joins with it's intended destination ?
This femoral artery branching (and destination joining) occurs identically in billions of humans ... and in each instance, the branch arteries always end up in the right spot.
That has to involve some kind of template and/or distance-angle information decision.

Wow, great post. This is exactly the type of thinking that keeps me coming back to ATS. I don't really have much to add, except that I've always wondered; once you get down to the "simple" moleculer level, what is the mechanism that causes the bits of DNA to combine and move around while trading information? It's all so impossibly complicated. If you threw a bunch of parts together, there is no chance that they would begin self assembling something that would become a car or a watch. What caused the first building blocks to have the impetus to begin forming a functioning thing in the first place? Why would they care to survive and begin organizing or to even exist? At what point do you get down to the simplest components?

Do we really know anything at all??

reply to post by tauristercus


I'm not a biologist, so I may be wrong in places and I certainly won't explain it well.

Growth and the formation of organs is chemically regulated much like bacteria control their populations. You can see the minor difference in results of this analog process in the differences between identical twins.

In effect different genes are activated at different times in a chain process which results in the growth of complex organs through chemical gradients and differentiation into different cell types, similar to how very simple genetic algorithms can produce complex systems. See Genetic Algorithms . Interestingly many of these growth relationships are based on Phi.

So in effect, DNA does store lengths and shapes using simple rules to create complexity. DNA also stores environmental information so information gleaned by my DNA will be passed on to my offspring. It is also possible that non-coding regions actually have a use and occasionally a new gene can be formed from the non-coding region.

Is this a satisfactory explanation?

[edit on 11/11/2009 by LightFantastic]

And what about the bilateral symmetry of the human body ... an arm, leg, ear and eye on one side of the body, and then essentially "mirrored" on the other side of the body.

It would make sense that the necessary information to create an arm, leg, ear and eye would have to be stored in the DNA just once and only angles would need to be changed to create left and right arms, legs, etc.

So effectively reducing to a minimum the amount of genetic data required to create those appendages ... just store the info for a right arm and then use the same info but change the necessary mathematical values. Otherwise it would require double the amount of info stored in the DNA, one lot of info for a left arm and a second almost identical info for a right arm.

Originally posted by tauristercus
It would make sense that the necessary information to create an arm, leg, ear and eye would have to be stored in the DNA just once and only angles would need to be changed to create left and right arms, legs, etc.

Yes we have a genetic code for an Eye for example (called eyeless). I believe this gene is the same in many creatures with eyes even though the eyes they produce are of different construction. There must be another chemical gradient in symmetrical organisms that tells this mechanism what side it is making for.

I have seen experiments where the code for antennae has been swapped for the code for leg, causing the creature to grow legs where its antennae should be with correct symmetry.

So it appears that there are marker genes that determine what parts go where, then "subroutine" genes that actually create the desired organ, using the symmetry gradient to determine which way.

Eventually we should be able to create a 3D rendering of an organism using only a sample of its DNA.

Edit to add: It is known that certain chemicals disrupt the chemical signalling and cause bith defects. Thalidomide is a good example that stunts certain parts of the growth process.



[edit on 11/11/2009 by LightFantastic]

Originally posted by warza
Wow, great post. This is exactly the type of thinking that keeps me coming back to ATS. I don't really have much to add, except that I've always wondered; once you get down to the "simple" moleculer level, what is the mechanism that causes the bits of DNA to combine and move around while trading information? It's all so impossibly complicated. If you threw a bunch of parts together, there is no chance that they would begin self assembling something that would become a car or a watch. What caused the first building blocks to have the impetus to begin forming a functioning thing in the first place? Why would they care to survive and begin organizing or to even exist? At what point do you get down to the simplest components?

Do we really know anything at all??

I often wonder the same thing myself ... that we know the basics of whats happening at a cellular level but deep down, we're really ignorant of whats really going on.

I like to imagine a cell magnified to the size of a football field and lots of activity going on ... but then I have to remind myself that there is NO one deliberately making things happening and that whatever happens inside the cell (football field analogy), has to happen in total darkness.

As an example, lets say its necessary for a protein to be created. The information for the protein structure is ultimately stored in the dna within the cell. So the cellular component that has to "read" the necessary portion of the dna can't just "look around, locate the desired part of the dna and then make it's way over to that spot". Everything has to occur randomly ... the cellular component can only access that part of the dna when it randomly comes in contact with it ... then "read" the necessary info from that spot, then has to wait for the necessary "raw materials" floating around within the cell to again randomly come within "reach" so that it can complete the manufacture of that protein.
Once completed, the protein in turn just moves around the cell randomly until it happens to reach the spot where its services are required.

I believe it happens thru a language of some 3,000,000,000,different genetic letters
encoded within DNA.



[edit on 11-11-2009 by randyvs]

reply to post by randyvs

This isn't something I have heard of before. Do you have any more information?

Originally posted by LightFantastic

Originally posted by tauristercus
It would make sense that the necessary information to create an arm, leg, ear and eye would have to be stored in the DNA just once and only angles would need to be changed to create left and right arms, legs, etc.

Yes we have a genetic code for an Eye for example (called eyeless). I believe this gene is the same in many creatures with eyes even though the eyes they produce are of different construction. There must be another chemical gradient in symmetrical organisms that tells this mechanism what side it is making for.

I have seen experiments where the code for antennae has been swapped for the code for leg, causing the creature to grow legs where its antennae should be with correct symmetry.

So it appears that there are marker genes that determine what parts go where, then "subroutine" genes that actually create the desired organ, using the symmetry gradient to determine which way.

Eventually we should be able to create a 3D rendering of an organism using only a sample of its DNA.

Thats great info and the concept of symmetry gradients very interesting indeed ... thanks for that !

But I find it very difficult to visualize how symmetry gradients can be used to create extremely complex organs such as the heart that have to be constructed to a certain precision ... chambers, entry/exiting arteries and veins can only be in a certain location ... any deviation and the heart is a no-starter organ.
We're talking substantive and solid, macro architecture here that surely has to rely on the absolute correct placement in 3D space of millions (if not billions) of cells. This in turn implies the possibility of some kind of underlying construction template being called into play.

Originally posted by randyvs
I believe it happens thru a language of some 300,000 different letters
encoded within DNA.

[edit on 11-11-2009 by randyvs]

Not quite that many letters are needed ... there are only 20 or so amino acids that are used to create all the possible required proteins within a cell and therefore only 4 letters are needed ... these being ...

A - Adenosine
G - Guanine
C - Cytosine
T - Thymine

These 4 letters give a total combination of 64 possibilities when using 3 letters at a time ... which is more than enough to code for the 20 amino acids.

reply to post by LightFantastic

As scientists began to decode the human DNA molecule, they found something quite unexpected—an exquisite 'language' composed of some 3 billion genetic letters. "One of the most extraordinary discoveries of the twentieth century," says Dr. Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle, Wash., "was that DNA actually stores information—the detailed instructions for assembling proteins—in the form of a four-character digital code" (quoted by Lee Strobel, The Case for a Creator, 2004, p. 224).

copy n paste but hey

reply to post by tauristercus


Here's the link have fun.Link
It works right?



[edit on 11-11-2009 by randyvs]

Originally posted by randyvs
reply to post by tauristercus

 

Here's the link have fun.Link
It works right?



[edit on 11-11-2009 by randyvs]

Oh, my apologies as I misunderstood that reference of 3 billion letters thinking that these might have been 3 billion "individual" letters ... actually they meant 3 billion instances of just those 4 A, G, C and T letters.

reply to post by tauristercus
No you do not owe me an apology partner. That was a misquote and a correction that I must apologise for.

Originally posted by tauristercus

But I find it very difficult to visualize how symmetry gradients can be used to create extremely complex organs such as the heart that have to be constructed to a certain precision ... chambers, entry/exiting arteries and veins can only be in a certain location ... any deviation and the heart is a no-starter organ.
We're talking substantive and solid, macro architecture here that surely has to rely on the absolute correct placement in 3D space of millions (if not billions) of cells. This in turn implies the possibility of some kind of underlying construction template being called into play.

The symmetry gradient only tells each growth system to alter is construction to be left or right handed.

I understand that if you visualise the human body as being trillions of many differnet cells organised in the correct position then it seems impossible.

Everything being in the right place is because each separate system branches or differenciates. For example the main arteries will grow first and part of these arteries will turn into the heart. These will then branch into the rest of the vascular system. Many other systems also start as a simple tube, such as the brain and the rest of the nervous system. The mouth to anus tube also does this, branching into the bronchia which branch into the lungs.

There is a basic template that much of life uses. It is the "plug-ins" that make everything different.

Good post by the way! Did you look up any Genetic Algorithm stuff? It is a good starting point to see how complexity can arise from very simple rules.

[edit on 11/11/2009 by LightFantastic]