Sunday, May 26, 2013

Whither Came We?

I apologize for not putting up a post last week. Without getting too deep into the personal space, life intervened.

Anyway: Back to Science!

At least one of my two readers may remember the series I did on Biological Revolutions. You may recall one I did on the transition of proto-life-as-we-know-it to the prokaryotes (See here.) and the rise of the eukaryotes. (See here.) From there I talked about when multicellularity occurred. (See here.) I made a leap then to neurozoans: animals who had differentiated a system of "perception" of the world that allowed integrated responses.  (See here.)

Now I left out many other Biological Revolutions in that series. One of which was the development of, well, development.

Organism development is the process by which a proto-organism, such as a zygote, develops into a larva and eventually into an adult. The core of this process is the development of an embryo, termed embryogenesis. Since an embryo is a proto-organism that is pre-directed towards developing into a larva, this is clearly the first step.

Most embryos begin as a zygote: an egg fertilized by sperm. Some embryos begin via parthenogenesis, in animals this starts asexual development from an unfertilized egg. The egg spontaneously doubles so that it resembles a zygote and development proceeds from there. This is called psuedogamy. There is a similar process in plants where pollination is required to get the ball rolling but the DNA of the pollen has no role in the developing embryo.

Regardless, once we have the moral equivalent of a zygote the process proceeds with the "goal" of a target embryo that can then continue to a larval or adult form.

When you think about it, embryogenesis is really, really strange. It starts with a single cell that looks not much different from a single celled organism. But it is programmed very differently. The zygote is packed with special proteins that are intended to shepherd the first few divisions of the cell into a multicellular collection of cells. There's a terrific experiment that one can do with frog eggs (I did this in college.) where you wait for the egg to do its first division and then carefully separate those two cells. Each of the two cells will then develop independently into a separate (and largely identical) frog.

This can occur for multiple divisions. Depending on the species and technique one can divide two, four, eight, etc., cells and get viable larval forms that grow into identical adult frogs. These cells are totipotent.. Any one of these cells can become any cell in the developed body. At some point, totipotency is lost and the cell becomes pluripotent. In animals, this means the cell can be become any cell in any of the three germ layers. Think of germ layers as the next step. They are also called primary tissue layers. At this point the embryo has formed a hollow sphere called a gastrula. (Before this it was called a blastula. I skipped that step.) The "layers" refer to the placement of the cells in the sphere. In animals, they are:
  • Endoderm: Forms the organs of the animal's internal tube such as the stomach, colon, liver, bladder, etc.
  • Mesoderm: Forms organs not associated with either the internal tube or external skin such as the circulatory system, kidneys, gonads, etc.
  • Ectoderm: Forms the organs associated with the outside skin. The skin itself, central nervous system, peripheral nervous system.
These pluripotent cells are the stem cells that everybody talks about.

This is the process for animals. Plant embryogenesis is somewhat different (See here.) but the overarching process is the same. A single cell proceeds to a larval form (i.e., a seed) which under the proper circumstances grows into an adult. (See here.) But I have to say I know animals better than plants so I'm going to stick to animals for the time being.

The critical feature here is the process by which the original single cell is programmed and the subsequent cells dance to each other's tune until the target stage is created. Remember, that there is no plan written into the genes. There are very few genes that are only used during development. Most of them are used throughout the organism's life. However, the choreography of development is exquisitely precise. I like to think of the genes as individual notes in a symphony where each note determines which other collection of notes is played.

Embryogenesis is the first step of a life cycle. Once you have an organism that can generate a life stage that can then act as a precursor to another life stage, changes can be introduced at one point that have knock on consequences down stream. The bones of the middle ear are called the auditory ossicles. There are three bones: the malleus, incus and stapes. Of the three, only one is used in the ear in reptiles. In reptiles it's called the columella. In mammals the columella is referred to as the stapes. The malleus derives from the lower jaw bone of earlier forms and is still there in reptiles and birds. The incus derives from the upper jaw bone.

In this case, "derives" means that if you take careful not of the process of jaw development in reptiles and follow the migratory path of the cells, you'll be able to identify the cells that form the articular and quadrate bones of the reptile jaw. If you follow the same cells in a mammal embryo, those same cells eventually become the incus and malleus. If you follow the cells that create the columella in reptiles you'll seem them form the stapes in mammals.

Where it can, evolutionary pressure ruthlessly forces efficiency. It is far, far cheaper to derive a structure from the embryologic development of an existing structure than create something new. Most vertebrate eyes derive from exactly the same tissue. One exception is the eyes of snakes (See here.)

The evolution of embryological development appears way back in the Cambrian (600 MYears ago.) The first clear fossil record we're familiar with is, in fact, a mark of embryogenesis. Of course, it happened earlier than the Cambrian since when we see Cambrian fossils it's already in full swing. (See here.) The article referenced talks about a bunch of circumstance that might have enabled or selected for embryogenesis but they do not address how these mechanisms might have happened in the first place.

Okay. Now I'm going to link this discussion back to the evolution of the prokaryotes and eukaryotes I mentioned in the beginning.

One of the interesting mechanisms that might have occurred to cause the creation of both groups is the creation of viruses. I mentioned in the prokaryote post that the majority of the DNA in the virus families has little similarity to the DNA the viruses target. Patrick Forterre has suggested that the viruses were instrumental in catalyzing the creation of the prokaryotes and may have been instrumental in the creation of the eukarotes. A virus happily floats around using cells to make other viruses and something breaks. It gets stuck in the cell. The virus DNA machinery becomes incorporated into the host cell and a new, hybrid, group is formed. His argument is the current viruses are those that didn't get incorporated into modern cell machinery and the modern cell machinery reflects viruses that did.

There is a type of virus that is abundant across the genome of various animals. These are endogenous retroviruses. "Endogenous" meaning part of the current genome. "Retroviruses" are those that are RNA based and then transcript into DNA. So the DNA that represents the ERV is the resulting DNA from an RNA virus. Some very interesting research has been published in the last couple of years showing that in humans, HERV (human  ERV) is a precise marker of pluripotency. (See here. And here. And here.) In fact, it is so active that there's evidence that HERV is, if not necessary, extremely important in stem cells. (See here. And here.)

HERV has been implicated in carcinogenesis, immunity and the creation of the placenta. (See here.)

This relationship to pluipotency is not limited to humans. It's been shown for other mammals as well (See here.) to the point that several scientists are wondering if the ERVs drove mammalian evolution. (See here.)

We don't have to stop at mammals. Two active endogenous retroviruses have been found in fruit flies: gypsy and tirant, though it's not clear if they're related to pluripotency. The research is still new.

But that never stops me from speculating.

What if the embryonic development derives from viral interaction with early eukaryotic cells? What if the reasons the phyla are so different from one another derives from the original root viral material that triggered their embryology?

What if we're really viruses underneath?
By the way, if anybody is interested in how we did in the solar vote last time: we won. Hard fought but we did better than the Senate with over a 2/3 majority.

Rationality triumphant.

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