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How can DNA determine morphology?

by pellman
Tags: determine, morphology
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pellman
#1
Jul17-14, 10:51 AM
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The following comes from a rudimentary understanding of DNA and biology. Correct me if I have wrong assumptions.

Each cell of an organism contains the same set of DNA as all the other cells of the body. Exceptions occur from imperfect copying but these are pathological.

Since not all cells are identical, so there exists some process whereby the same DNA functions differently to produce different kinds of cells. However, at some level we can identify sets of cells which are for all practical purposes identical. Maybe, for example, all human femur bone cells are identical. Or maybe within the femur the cells at one end are different than the cells at the other. However, at some level, large compared to the size of an individual cell, the cells are all identical to their neighbors.

Consider such a section of tissue. It has a morphology, a shape that is essential to its proper function. Whatever this shape is, at the scale of an individual cell, the shape cannot be "known." If we speak for a moment as if the cell has a brain and that brain is following the instructions of the DNA "map", I don't see how the cell can "know" how to behave relative to its neighbors in such a way that they collectively produce the necessary large scale shape. Because the cell can only "know" what its nearest neighbors are doing. It doesn't "know" where it is in the overall shape it is working to produce.

Even if each cell had a map of the organ detailing the specific role of every cell in that organ, it would be impossible for the cell to be able identify on the map which cell it corresponds to. And each cell has the same instructions as every other cell. There is no central director communicating separate instructions to the cells.

Take a femur for instance. Bone cells on the surface of a femur might be able to "know" they are on the surface of the bone and so they don't reproduce in such a way that the bone would grow deformed. But how do the cells on the ball of the femur know to arrange themselves nearly spherically while those on the shaft of the femur are arranged nearly cylindrically. They can't possibly know that. And there is no central director with a "big picture" telling them how to do it.

So I don't see how in principle that DNA alone can determine gross morphology. If anyone here can explain it, I'd be very interested.
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SteamKing
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Jul17-14, 11:56 AM
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Quote Quote by pellman View Post
So I don't see how in principle that DNA alone can determine gross morphology. If anyone here can explain it, I'd be very interested.
The answer is simple: DNA is not the sole determinant of gross morphology of an organism.

At best, think of DNA as a biological filing cabinet which contains all the plans and specifications for making a human or a turtle. Just like the plans for a building don't actually turn into a structure by themselves, so too DNA requires additional mechanisms to turn the plans for building a cell into an actual biological entity.

When a new animal organism is conceived from the mixing of its parents' DNA, a series of biological processes begin to occur as the fertilized egg cell divides and starts to grow into an embryo. When the embryo develops, the basic plan of the organism is created using many different biological processes:

http://en.wikipedia.org/wiki/Developmental_biology

The cells in the developing embryo communicate with one another by a variety of means as different types of tissue begin to differentiate from the original egg cell. Some of the undifferentiated cells are called stem cells:

http://en.wikipedia.org/wiki/Stem_cell

Depending on the exposure to specific biological signalling chemicals, the stem cells turn into bone or muscle tissue or an organ like a kidney. The signalling chemicals with which most people are aware are the various hormones coursing through our bodies, but there are several other lesser known substances. An increase in a specific hormone, like testosterone, can lead to a deeper voice, increased muscle mass, and hair in inconvenient places.
Ygggdrasil
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Jul17-14, 10:36 PM
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How do you go from a single cell (the fertilized embryo) to a complex multicellular organism? Well, first, the embryo needs to define the various axes for its body plan (front-back, top-bottom, and left-right). Often these axes are defined by gradients of signaling molecules (called morphogens) that are produced on one side (leading to a high concentration for example at the side that will become the head) and diffuse away while being slowly degraded (leading to a low concentration at the side that will become the tail). This allows cells to know where they are in the organism just by measuring the concentration of a signaling molecule.

Another important concept here is differentiation. Although all cells contain the same DNA sequence, the cells can modify which regions of DNA are accessible to be read. For example, DNA sequences can be chemically modified (methylated) to silence those regions of DNA, and different cell types will have different DNA methylation patterns. DNA methylation and other types of epigenetic marks are important for telling cells which genes to turn on and which genes to turn off, thus determining which type of cell they become.

Thus, once the embryo begins dividing, the morphogen gradients will let cells know where they are in the embryo. Based on their position, they then can then begin differentiating into the proper cell type by turning on and off the proper sets of genes. The process is much more complicated than that, but this at least gives some insight into the basic mechanisms that occur during development.

The organism for which this question has been best studied is the worm C. elegans. Every C. elegans consists of 959 or 1031 cells depending on the sex, and every cell division leading from the fertilized embryo to the full adult has been mapped. Thus for every single cell in the adult worm, we know exactly the sequence of cell divisions that led up to that cell having its particular position in the adult embryo.

gravenewworld
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Jul18-14, 06:55 AM
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How can DNA determine morphology?

The problem is that you fall into the trap that many scientists do when it comes to biology--reductionism. DNA is only one part of a much greater machine and in fact, I'd argue there exist much more complex systems within a cell than DNA. Some strains of rice have more genes than humans do, but who'd argue that rice is more complex than a human? The failure in logic is that DNA does *not* encode all of the information needed to produce a cell. DNA only produces proteins, but that tells you nothing about how those thousands of proteins interact as a system. Those proteins then go on to produce a system of millions of metabolites and millions of post translational modifications that truly describe the physiology of a cell. Many biochemical pathways, when viewed holistically, serve as biochemical supercomputing biosensors that tells DNA what to do. These biosensors can respond to everything from mechanical forces to nutrition or hormone gradients. You can not understand the concept of a symphony by examining the conductor alone.
pellman
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Jul18-14, 07:42 AM
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Thanks, guys. This is very complex.
Ygggdrasil
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Jul19-14, 04:46 PM
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Quote Quote by gravenewworld View Post
DNA only produces proteins, but that tells you nothing about how those thousands of proteins interact as a system.
But isn't information about how these proteins interact with other proteins and function in the cell ultimately encoded in the DNA? Just because we don't know how to determine that information from a DNA sequence doesn't mean that it isn't there.
DiracPool
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Jul19-14, 05:08 PM
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Quote Quote by pellman View Post
Thanks, guys. This is very complex.
If you're really interested in this question, pellman, I would suggest picking up the book, "Endless forms, most beautiful" by Sean "B." Carroll. The B is to distinguish this guy from the other Sean Carroll, of GR physics fame. Embryology IS very complex. It's complex and magical and wonderful. In "Origin of species", I think that the last line of the book or something, "endless forms most beautiful."

Whatever it is, that book will answer your question. Another good book is "Your inner fish" You can't just look at the DNA of cell in isolation in order to understand how it creates an organism. It very much is interweaved with the environment in the manner in which the DNA expresses itself during development. This is what they call the science of evo-devo. But Carroll's book goes deep into that, and it's a relatively easy, popular read.
SteamKing
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Jul19-14, 07:41 PM
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Quote Quote by pellman View Post
Thanks, guys. This is very complex.
And that's why were still figuring out some of it, we have no idea about a lot of it, but a tiny bit we're still pretty sure of. The amount of new information added in just the last 30-40 years is staggering, particularly since DNA replication techniques were developed.
Torbjorn_L
#9
Jul20-14, 10:00 AM
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Quote Quote by pellman View Post
If we speak for a moment as if the cell has a brain and that brain is following the instructions of the DNA "map", I don't see how the cell can "know" how to behave relative to its neighbors in such a way that they collectively produce the necessary large scale shape. Because the cell can only "know" what its nearest neighbors are doing. It doesn't "know" where it is in the overall shape it is working to produce.
If you substitute water molecules for cells and a water drop for the organ, the problem with the attempted description may become clearer:

'If we speak for a moment as if the water molecule has a brain and that brain is following the instructions of the force "map", I don't see how the water molecule can "know" how to behave relative to its neighbors in such a way that they collectively produce the necessary large scale shape. Because the water molecule can only "know" what its nearest neighbors are doing. It doesn't "know" where it is in the overall shape it is working to produce.'

Other comments have described how the organ shape ("water drop shape") emerges out of small scale interactions. The cell doesn't know what it is part of any more than the selfish genes that are the core of the evolutionary process today. They only "know" what they have to do to survive and procreate (through the germ line), painfully learned by trial and error or success, differential reproduction, through each generation. It is the environment (for each gene all the other genes and the rest of the nature it lives in, for each cell all the other cells and the rest of the nature it lives in) that contains the rest of the information that allow structure formation.

Quote Quote by gravenewworld View Post
The problem is that you fall into the trap that many scientists do when it comes to biology--reductionism. DNA is only one part of a much greater machine ...
That depends on what you mean by "reductionism". If you mean the method to divide and conquer, science is based on that and as I showed by a water drop example above biology is no different from physics in that respect.

If you mean a philosophic claim that disallow emergence, that too fails as per the example.

And finally the water drop example shows how emergence, of structures like galaxies, stars, planets, geophysical systems, cells and complex multicellular organisms, is part and parcel of "divide and conquer".

Also, the "reductionism" of the selfish gene vs the environment is a better model than your definition of "holism" which fails miserably here. The organism machine(s)* and their sensory networks aren't all of the environment, and is too small a concept to describe evolution as it forgets to cover the here necessary entirety of the system. Differential reproduction incorporates everything from developmental defects (it better has) to accidents (some of which are avoidable).

*I would quibble with the idea that a set of cooperating machines are "a" machine rather than a system, there is a feature creep in that definition (likely because if it is philosophy it was never intended to be tested), but the idea has worse problems and never gets off the ground.


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