After fertilization, the zygote begins to divide, duplicating all 46 chromosomes faithfully each cell division so that every daughter has the same genetic material. At first there is no growth, and all the cells are the same, so that the size of the cells gets progressively smaller as their number increases. The cells keep dividing until there is a ball of cells. At this stage, every cell is pluripotent, meaning that any one of these cells, if separated from the others and placed in a nurturing womb, could develop into a normal baby. This means that the cells are not yet determined to become a particular type of cell, and since they are all the same, and not specialized yet into any particular type, they are also not yet differentiated. Identical twins occur at this point when something causes the undifferentiated, undetermined small ball of cells to come apart into two, each of which then continues to develop normally. Since all the cells have the same genetic material, the resultant individuals will be genetically identical. One could take this ball of cells and separate it into three parts, getting identical triplets. One could separate it into four parts, and get identical quadruplets. The point is, each of these cells, and any group of these cells, is capable of building an entire, normal individual. They are pluripotent stem cells, one of the types of embryonic stem cells you have heard so much about.
As the cells continue to divide, the ball begins to hollow out, and soon the hollow ball loses its complete symmetry as one side pushes into the interior of the ball so that some of the cells are on the “outside” of the ball and some of the cells are on the “inside”. At this stage, the cells begin to be determined, meaning that their instructions in their nuclei begin to be “set” irreversibly so that they become destined to become a certain class of cell, and lose their original capability to make every possible type of human cell. If you think of each type of cell deriving from some other type of cell, like branches off a tree with each smaller branch representing a more particular type of cell, the zygote (fertilized egg) is the trunk, and has the capability of developing into every type of human cell. It is therefore the ultimate “stem cell”, since all other cells “stem” from it. At very early stages, when the embryo is still microscopic, some of those cells become committed to become skin and lining cells, some commit to becoming nerve tissue, and some commit to becoming bones and muscles, though at this stage they still all look the same. The fact that they are committed means that they have become determined, and cannot go back to being pluripotent zygote-like stem cells. They are still stem cells, because they will give rise to yet more specific cells and retain the capability of being several types of cells, just not ALL types of cells. They might, for example, become a bone cell or a muscle cell, but can’t any longer develop into skin cells or brain cells. Since they aren’t yet actually bone or muscle cells, they are not yet differentiated, but their internal program is now set for a certain pathway of development, so they are determined.
The rest of the development of the embryo is a matter of continually narrowing capabilities of the stem cells, as they become more and more narrowly committed to a certain type of tissue. Also, the cells begin to look and act differently from one another, becoming differentiated into specific mature cell types. By the time of adulthood, the individual still has many stem cells scattered throughout (probably) all his tissues, which serve to heal injuries and replenish losses. Most of these stem cells are still very determined (that is, they are committed to a certain type of tissue), however, and very hard to isolate. The different types of blood cells are being continually formed from stem cells in the bone marrow, but these stem cells can only “branch” into specific types of blood cells, and couldn’t become skin cells. There are other stem cells scattered in our skin that can regenerate a few types of skin cell. For example, it is now thought that there may be some stem cells even in the heart, so that under the right circumstances cardiac muscle might be regenerated. Our livers already do a pretty good job of regenerating themselves, presumably from residual stem cells that are capable of becoming the various types of liver cell.
Returning to our metaphor of the nucleus as blueprint library, we can think of the librarians (the regulatory proteins that "tend" the DNA) as controlling very tightly the set of blueprints that can be accessed in each cell. One can think of them unlocking and locking various drawers, so that only certain blueprints are available in that library (that cell nucleus). At fertilization, they gather together the filing cabinets from the father and the mother's germ cells, and begin to open certain drawers that contain plans for molecules and building materials needed for formation of the ball of cells, and they lock up the drawers that have plans for very specific cell structures like nerves and bone and skin, that are not yet needed. As the contractor molecules come in for plans, they can only get those that have to do with being an embryo and setting up the framework for the organism as a whole. At some point, for reasons we do not completely understand, having to do with size and age of the embryo and with the position of the cell within the embryo, some of the librarian molecules in some of the cells open some new drawers, and lock up some old ones. The new drawers have plans for new structures, new molecules, new cellular machinery that will make the cell differentiate into a particular kind of cell, and the locking of the older drawers means that there is no going back now; the cell has been "determined" to the extent that the drawers for the earlier functions are now locked and inaccessible. As the cell divides and the "libraries" are duplicated, the librarians are duplicated also, so that the daughter cells will have the same drawers open or locked. An adult stem cell is a cell that keeps some of the earlier drawers open, in case injury necessitates the small-scale regeneration of some particular tissue.
The interest in stem cells derives from the observation that some animals, such as salamanders, can regenerate entire limbs, while we cannot. Why can we not? It appears that whatever stem cells we have retained, there are none “primitive” enough, none close enough to the original embryonic stem cells, that can recapitulate the original process and generate and direct the whole set of cells and processes needed to reconstruct the damaged limb or organ. The irony, of course, is that we know that the whole instruction set is “in there” in the DNA, we just don’t know how to push the “reset” button, so to speak. Those early blueprints, the parts that originally constructed our nervous system, musculoskeletal system, GI tract and skin all from a single featureless cell, are somehow there but “locked up”. Stem cell research is all about trying to learn how to turn these organ-construction programs back on again. It is about identifying those circumstances that push the "librarians" to return a given cell back to a pluripotent state, unlocking the very early file drawers and undoing its determination as a particular type of cell.
(This continues here...)