Tag Archives: evolution

The Differentiation Code.

Our newest embryology related publication is now out. It is especially nice to get this out given the scare we got last June.

The Differentiation Code

Richard Gordon, Natalie K Gordon

Abstract

In code biology we seek a presumably arbitrary, and thus symbolic relationship between two or more entities, such as the relationship of the DNA triplet code to amino acids. Here we review the differentiation code from the code biology point of view. We observe that lineage trees of mosaic organisms can be subsumed as special cases of differentiation trees of regulating embryos. The latter can be empirically discovered as a bifurcating tree of contraction and expansion differentiation waves that recursively divide the embryo into its cell types. A binary digit, 0 or 1, assigned to each wave results in a binary number corresponding to each cell type, and may be called the differentiation code for that cell type. The differentiation tree has a correspondence in the genome, in terms of the genome’s logical structure. For a given cell type, the path to it from the zygote is marked epigenetically on the genome. Thus the differentiation code symbolically maps an epigenetically marked subset of the logical structure of the genome to the phenotype of a particular cell type. The waves involved and signal transduction from the cell state splitter to the genome are intermediaries in this relationship, and may also be arbitrary choices, and thus part of the code. In full, differentiation code = history along the differentiation tree of the differentiation wave types leading to a given cell type ⇔ contraction or expansion of the cell’s cell state splitter ⇔ activation of one of two signal transduction pathways from the cell state splitter to the nucleus ⇔ activation of one of two readied gene cascades (the “nuclear state splitter”) ⇔ epigenetic marking of the selected portion of the logical path. Each wave is in effect a cybernetic control system that results in differentiation of a set of cells and initiation of two new waves (cybernetic systems) as its goals. The differentiation code forms a basis for open evolution and its appearance was one of the major evolutionary transitions.

Embryogenesis and the G-d Factor.

Many years ago Dick and I reached am impasse on our research on the waves. We had the image of the wave on the top part of the ectoderm but we couldn’t actually see the bottom half. Our engineer collaborator said the wave must cover all the ectoderm and therefore could not be THE differentiation and organizing signal. I said our engineer was wrong. I had observed enough embryos that I just knew the wave did not go all the way around the embryo. I was absolutely certain I was right.

We had an argument over it. It started at work and it continued after we got home and the kids were in bed. Now normally we never argue. We have these very rational easy going discussions about everything from laundry to dishes. This time we ended up shouting at each other into the wee hours of the morning. Neither one would back down. In the end we concluded that the only thing to do was more research. We  did top and bottom pictures simultaneously and it turned out I was right. End of story.

There was one tiny issue. The next morning after our huge argument our neighbour came over for coffee with the wife of the newly wed couple who had just moved in next door. As soon as Dick left and she asked me if I was all right. Was I injured? Had he hit me? We had been yelling so loudly we had awakened her. She was so worried about me! How embarrassing. I had to assure her we were only arguing over data interpretation and we had concluded the way to settle the argument was to do more experimental work. She left, somewhat reassured but still dubious, and we made a decision to be certain the windows were closed if we ever needed to fight over data interpretation like that again. We never did have such an argument because we both learned an important lesson. The embryo is always right and when you have a disagreement you must always go back to the embryo to settle it. (I only occasionally rub it in that I was right.)

wedding-12a-1

From our giddy newlywed days and our only really ferocious argument.

The second worst debate we ever had was over the G-d factor in our book. Dick is an avowed atheist although he does occasionally stray off that stance and exhibits more of an agnostic position. Although I am no biblical literalist,  I am a religious person and I deeply and absolutely accept the idea of a higher power I call ‘The Master of the Universe’ according to my beliefs. In preparing our book I really wanted to make sure we acknowledged the Master of the Universe.

I wrote the first draft of Chapter 1 and every time Dick did his round and he removed the G-d factor. I would review his work and put the G-d factor back in. This went round and round quite a few times. He argued there is no place for a G-d factor in a purely scientific book. He is right but this is also MY book and we were gong to have that G-d factor. One reason I was so intent on having it in there is I am not alone in being both a scientist and being a religious person and I often feel the lack of acknowledgement of the Master of the Universe in science. It’s like one can’t be both religious and scientific which is obviously untrue. I have a lot of company.

My first mentor in embryology was Hans Laale and he was also a deeply religious man. On his desk was a picture of his parents and a rosary bead hung on that. he kept his religious beliefs out of the classroom but he did acknowledge them once. About half way through his course, when I was having  deep philosophical discussion, he complained how hard the problem of embryology was and he said he wondered if the problem would ever be solved. Maybe there were just some things that we weren’t meant to know.

I disagree. G-d has created this universe with a set of rules and regulations, constants and laws. They may be hard for us to understand but as we grow and learn as a species I see absolutely no reason we should not be able to figure out exactly how the Master of Universe did it. Nor would figuring it out in any way diminish the glory of His creation. In fact I think greater understanding will only serve to increase our appreciation for Him.

We talked a lot about the problem over the years together. I like to think that at least in part, Dick agreed to co-edit a book where creationists and scientists debated the origin of life because of my influence. There is an interesting story he references there which we first heard from a rabbi. It is about a scientist who has been climbing the mountain of ignorance seeking answers to how the universe works. He arrives on the mountain top to find a lovely flat spot. And there, sitting around a fire discussing the problem, is a group of theologians (Jastrow, 1992). Dick’s book ended up creating more questions than answers but at least they got to questioning.

dina

From this process Dick acquired enough respect for theology that although he maintains his personal firm stance as an atheist, he was nonetheless ready to compromise with me and eventually allow me to keep the G-d factor in the book.

Dick and I added the following paragraph we could both agree on;

“The religious among us who nonetheless embrace the overwhelming evidence for evolution often see the finger of G-d as stirring that primordial goo: yes, life did start out as goo somewhere in the universe, maybe more than once, but it could only have done so because G-d did it. … And if one must invoke G-d, then we can at the very least, expect to figure out exactly how He does it.”

And that is the how and why of the brief appearance of the G-d factor in Embryogenesis Explained.

Book Excerpt: Why Evolution is Progressive

85597_evo_resources_resource_image_251_original

Image is from  University of California Museum of Paleontology’s Understanding Evolution

One of the outstanding recent scandals of biology has been the notion that evolution is not progressive, a concept that flaunts the evidence of our eyes. Any reading of the fossil record shows simpler starts followed by increasing sophistication, along many lines. Even where morphology doesn’t appear to change, competition between organisms can lead to an arms race, known as the Red Queen hypothesis from the children’s book Through the Looking-Glass, and What Alice Found There: “Now, here, you see, it takes all the running you can do, to keep in the same place”. Overall, there is indeed an increase in biodiversity over evolutionary time which we could delibately maintain. To be sure, there is some apparent backsliding, as when an independent organism, even a bacterium, becomes a parasite, or parts become vestigial or discarded, or features disappear and recur in closely related species, or a comet or an asteroid wipes out 95% of living species. But on the whole, some species in each branch of the tree of life tend to march on with richer diversity of structure and perhaps behavior. One caveat is that the total number of species, though perhaps not their complexity, may have peaked 530 million years ago, due to subsequent extinctions.

Those that stay behind may not progress, or at least not appear to do so in morphology. The most blatant example of the latter is that we are descended from bacteria, yet there are still plenty of our brethren bacteria around. And while we can’t be sure yet that modern bacteria are any more complex than the earliest ones, it is clear that the number of niches they live in has increased, and the corresponding biochemical and genetic diversity amongst bacteria has evolved. The diversity of minerals has increased with the evolution of life, so for example we can expect a parallel increase in the number of environments on minerals for bacteria, let alone environments in and on other organisms, in the evolution of bacterial film communities, symbioses and communities on and in eucaryotes that have been called symbiocosms. The heterogeneity and geographic separation of places that bacteria can live contributes to their diversity, and many have been classified as extremophiles or polyextremophiles for the extreme environments they live in. Therefore progress may be occurring at every level.

Some work on progressive evolution has been couched in the language of “increase in complexity”, and thus centers around the construction of measures of complexity and empirical data on whether complexity is increasing. For example, John Tyler Bonner counted the number of cell types in an organism as a measure of complexity. In our work, because of the direct link between the number of cell types and the number of differentiation waves, this count is clearly a measure of both differentiation and morphogenesis, i.e., it operates at widely different size scales. On the other hand, the differentiation tree is not a linear, but rather a branched structure, so it is not subject to simple, scalar measures of complexity. The problem of estimating the complexity of differentiation trees in a way that allows comparison is a subset of the problem of complexity of networks, which is under active investigation. Insofar as the differentiation tree is the genetic program of the organism, a bifurcating alternation of molecular events and physics (differentiation waves), it may be possible to calculate its algorithmic complexity, defined as the length of the shortest computer program that successfully mimics embryogenesis.

“Progress” became a dirty word in biology because it smacks of “purpose”, and the implication that the purpose of evolution was to produce us. The concept suggests that evolution indeed has a direction, which to many religious people (including many scientists), means “God did it”. Thus, for a biologist to speak of progress is said to play into the hands of the creationists and the Intellegent Designers (who distinguish themselves from other creationists by not uttering the word “God”). Rather than take this head in the sands approach, we will confront progress in evolution in this chapter.

On the question of the centuries old debate of the relationship between science and religion, we stand firmly in the belief that the universe is one, deserving one unified explanation that works, and do not opt for the so-called “Nonoverlapping magisteria” or “…lack of conflict between science and religion due to the lack of overlap between their respective domains” . That is an imaginary line in the sand. Attempts to draw it, or to claim the whole territory, from either side, are failing. Rather than propose a God of the gaps or science of the gaps, we prefer to push our investigations as far as we can with testable hypotheses, and leave the gaps of both kinds for later generations to work on.

Our plan in this chapter is, then, to delve into the evolutionary consequences of differentiation waves, ending with a plausible demonstration that they may be responsible for progress in evolution.

Introduction to Chapter 11, Why Evolution is Progressive, in Embyrogenesis Explained.