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Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress

Longer post today. Bear with me. [For a little background, be sure to read Understanding Ontogenetic Depth, Part I.]

1. What Does "Traversing Ontogenetic Depth" Mean?

Let's look again at Toy Organism Alpha. Figure 1 depicts a complete cell lineage -- "complete" in the sense that the starting point is a single cell, and the end point, a reproductively capable adult. Adults, by definition, can produce the specialized cells (gametes), which, when fertilized, start the whole process of cell division and differentiation again.

Toy Organism Alpha1.jpg

Figure 1

Once upon an evolutionary time, this lineage did not exist. (Alpha is only an illustration, of course; I mean cell lineages such as are found in real animals, which are vastly more complicated.) It had to be constructed, incrementally, by some undirected process. Under textbook neo-Darwinian theory, that process was descent with modification via the natural selection of randomly-arising variation. I'll refer to this theory by the shorthand "natural selection." Traversing ontogenetic depth means simply that any candidate evolutionary process (natural selection, genetic drift, self-organization, whatever) must build across -- "traverse" -- a distance of increasing complexity, from an aboriginal single-celled state, to multicellularity, to a genuine dividing and differentiating lineage. That distance cannot be crossed in a single increment of change.

Now, before we consider what natural selection requires, let's strip down Alpha's cell lineage to just the first two rounds of cell division, yielding four cell types:

Alpha mini lineage.jpg

Figure 2

This will provide our model for the problem of traversing ontogenetic depth via natural selection. Recall that the process of natural selection (Endler 1986) has three jointly necessary and sufficient conditions, which may be expressed by the following conditional:

If, within a species or population, the individuals


a. vary in some attribute or trait q -- the conditions of variation;

b. leave different numbers of offspring in consistent relation to the presence or absence of trait q -- the condition of selection differences;

c. transmit the trait q faithfully between parents and offspring -- the condition of heredity;

then the frequency of trait q will differ predictably between the population of all parents and the population of all offspring.

Could this process have constructed the mini-lineage in Figure 2? Let's see. We're going to try to traverse ontogenetic depth, step-by-step, via an undirected process. We can set aside for the moment condition (b), selective differences, and focus just on conditions (a) and (c), variation and heredity.

The starting point will be a single cell -- call it Cell Zero -- which divides:

cell zero.jpg

Figure 3

But that won't work for building the lineage, unless the daughter cells remain physically connected. So Cell Zero needs the instruction, (1), "divide and stick together." Obviously, this instruction must be in place before Cell Zero divides.

cell zero instruction 1.jpg

Figure 4

Now we have two daughter cells, but they're identical. Unless we provide another instruction to Cell Zero, however, we're going to produce a clonal mass of identical cells: no differentiation will occur, which we need to construct the lineage. Cell Zero therefore needs another instruction, (2), "daughter cells differ," which again must be in place before Zero divides.

cell zero instruction 2.jpg

Figure 5

Then the two daughters divide, yielding four cells of four different types. Have we successfully constructed the lineage via natural selection?

No; to this point, natural selection has caused nothing, because one of its necessary conditions, heredity, has not been satisfied. This organism (of four differentiated cells) must leave progeny, to which it transmits its distinctive variations. Condition (c) of the process of natural selection, heredity, requires that variations arising in a parent be transmitted to offspring. Heredity thus entails that at least one of four cells keep track of the instruction set for the lineage as a whole, if the cycle of differentiation is going to repeat (i.e., be maintained) in the next generation.

Cell Zero therefore needs yet another instruction, (3), in place before it divides: "One cell line must keep track of the whole instruction set, and become the starting point for another cycle of differentiation." This is the functional reason animals need something like a germ line (i.e., cells which produce gametes): those cells will be the instruction-minders, or instruction-carriers, for the organism as a whole.

cell zero instruction 3.jpg

Figure 6

Is natural selection operating yet? Nope: thus far, we're building an egg, namely, Cell Zero, by loading it with the functionally necessary instructions that must be in place before it divides. Reproduction of the whole lineage, which will enable selective differences (condition b) to arise, is causally well downstream. Whatever instructions must be present in Cell Zero, therefore, have to be there BEFORE natural selection can operate.

cell zero natural selection isnt operating.jpg

Figure 7

We've just traversed a relatively short interval of ontogenetic depth (OD). And the process of natural selection, harsh mistress that she is, stands entirely to one side, indifferently watching us do the work of building an egg. Not until we have produced a lineage capable of replicating itself with fidelity can natural selection begin to operate.

2. Try This Yourself, With a Pencil and a Sheet of Paper: P.Z. Myers Already Gave Me His Solution, Which Doesn't Work

There's nothing especially biological about all this. Figures 3 through 7 depict a decision tree, and what would be required, as instructions in the starting node (Cell Zero) to specify that tree and cycle it through successive generations. You can build such trees yourself, to any degree of complexity your patience will tolerate. Try to find the minimal set of instructions required in the starting node to generate the differentiated end-nodes, and to repeat the process from any one of those end-nodes. Keep in mind that, if you want the whole lineage to repeat ("reproduce") with fidelity, any decision affecting any end-node must be front-loaded into the starting node.

In late July 2004, at the Society for Developmental Biology annual meeting, held at the University of Calgary, P.Z. Myers and I talked about this very problem, at length. Myers stopped by my poster (which he pronounced wretched, by the way) and we found ourselves discussing what the "Urbilaterian" -- the putative ancestor of the bilaterally symmetrical animal phyla -- might have resembled. (In my poster, I argued that no one had successfully described Urbilateria because it is impossible to do, an argument I endorse even more strongly today.) Since Urbilateria, if it existed, would have been a metazoan and undergone a developmental process of its own, Myers and I wrangled about how that process would have evolved de novo -- just the problem we've been sketching above.

Myers told me I had greatly exaggerated what was a boringly simple puzzle. To illustrate his point, he drew me a picture (which I still have somewhere, I think), that looked like this:

PZs solution.jpg

Figure 8

"It's no real problem, Paul," Myers said. "Start with a eukaryote that becomes colonial. The cells of the colony start specializing, maybe a central cavity forms, and then some of the cells repress their gene expression and become a kind of germ line for the rest of the colony, which is evolving into a true animal. No big deal."

I have to admit when Myers told this story, he expressed it with such aplomb that, at the time, I could only smile. But as I contemplated his drawing, I realized what he had sketched could not possibly work in any realistic evolutionary scenario.

Indeed, it then struck me that I had seen Myers' scenario many times before. Evolutionary developmental biologist Lewis Wolpert -- whom no one, even in his wildest delirium, would ever mistake for an ID theorist -- had long critiqued the scenario on functional grounds, using what he called "the continuity principle." (1994) The continuity principle requires that any change occurring in an evolutionary transformation be biologically possible, that is, viable and stably heritable in the next generation.

"Since embryonic development requires the formation of a multicellular organism from a single cell," Wolpert observes (1994, 79), "the origin of the egg is a central and sadly neglected problem." The functional challenge to be solved is the origin of heritable differentiation:

The key to all development is the generation of differences between the cells, that is, making them non-equivalent [see Figures 1 and 2, above]. Only if the cells are different can the organism be patterned so that there are organized changes in shape, and cells at specific sites differentiate into different cell types. How could this have evolved? (Wolpert 1994, 80)

Look again at Figure 8, and think about what would need to happen between the "colonial" stage and the origin of the germ line (the red cell at the third stage). What mechanism is coordinating gene expression among all the members of the colony, such that only one cell lineage will evolve to carry the complete instruction set required to specify the form of the whole? How are mutations -- occurring in all individual cells of the colony -- transmitted to the next generation? If individual cells continue to reproduce via normal fission, or budding, notes Wolpert, "cell lineages [will be] mutating in all sorts of directions in genetic space." (2002, 745) Given such genetic chaos, he argues, "we consider it practically impossible" for the collection of cells to "yet retain the ability to evolve into viable new forms."

To modify irreversibly the global form of any animal, Wolpert contends, requires mutations affecting a single key cell -- the egg. Mutations affecting somatic cells -- especially when every cell, during the transition from colonial organism to true metazoan, is possibly either "somatic" or "germ line" -- cannot be coordinated:

There is no way that the genes in the huge number of cells...can change at the same time, and mutations in individual cells mean that they no longer share the behavioural rules of the majority. It is only through a coherent developmental programme, with all cells possessing the same genes, that organisms can evolve, and this requires an egg. (2002, 745)

At the moment, the problem of the evolutionary origin of cellular differentiation stands open, for the reasons outlined above. "How cell types of multicellular organisms came to be differentiated," noted Carl Schlichting (2003, 98), "is still an open issue." The problem, I think, cannot be solved within a neo-Darwinian (natural selection) framework, given that selection as a causal process cannot fix variants whose selective differences (condition b of selection) lie in the future. Building de novo the distantly end-directed pathways that characterize animal development, however, seems to require fixing just such variants.

To recapitulate my thesis, then:

The theory of evolution by natural selection does not explain the origin of animal form, because natural selection cannot account for origin de novo of the developmental stages required to construct (i.e., evolve) animals. The concept of ontogenetic depth helps us to understand why.

There's a lot more to say, but this outlet doesn't favor the long form. Let me end, however, with one final point, which I'm hoping P.Z. Myers will address.

3. How Does Early Development in Animals Evolve?

It is unclear how ontogenetic architectures early in metazoan history could have differed fundamentally from present-day systems. The problem may be summarized as follows:

-- There are striking differences in the early development in animals, even within classes and orders.


-- Assuming that these animals are descended from a common ancestor, these divergences suggest that early development evolves relatively easily.

-- Evolution by natural selection requires heritable variation.

-- But heritable variations in early development, in major features such as cleavage patterns, are not observed.

Extant species provide many case studies in the puzzle of modifying early development. Remarkable examples of early ontogenetic divergence abound (e.g., in nematodes; Felix 1999; Schierenberg 2001). These divergences have now become a commonplace of the evo-devo literature, and are taken as prima facie evidence that early development evolves dramatically. "It is clear that a casualty of [these comparative data]," argues Davidson (1990, 384), "is the 19th century concept that early development must be an evolutionarily conserved process" -- a concept, interestingly enough, which Davidson himself advocated in 1971: "One can imagine modest alterations or additions to the early parts of the developmental program," he wrote at the time, "but it would be very unlikely that such programs could be supplanted." (1971, 131)

There exists a striking paucity of experimental evidence showing heritable variation in what Wimsatt and Schank (1988) call the "deeply-entrenched" features of metazoan development. Why is such deep variation so hard to find? Again, we should ask, what does the logic of natural selection require?

A. Variation in a trait q

B. Fitness differences in consistent relation to the presence of trait q, and

C. Heritability of trait q.

The experimental literature on model systems such as Drosophila describes many mutations in early developmental characters and patterns. With rare exceptions, however, such mutations are not heritable, in the sense that the phenotypes exhibited do not survive as stably-breeding lines. As a result, some have argued that we should not expect mutagenesis to reveal the basis of adaptive variation: "The take home message," argues Nagy (1998, 820), "is that mutagenesis in model systems does not undo evolution or reveal, in any direct fashion, the basis of evolutionary change."

But if the experimental literature does not provide evidence of heritable deep variation, how do we know that such changes are even possible? "Comparative embryology abounds," argue Wray and McClay (1989, 811), "with empirical evidence of evolutionary modification of early development." The theory of common descent, of course, underwrites the assumption. Because the animals are believed to have descended from a common ancestor, therefore it must be possible for early development to vary heritably. "So the dilemma is easily solved," argues Thomson (1992, 112). "Because early stages have changed, they must be capable of change."

But what if the evidence from model systems continues to suggest that fundamental variation in early ontogeny is not heritable?

References

Arthur, Wallace. 2004. Biased Embyos and Evolution. Cambridge: Cambridge University Press.

Britten, R. and Davidson, E. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quarterly Review of Biology 46:111-38.

Davidson, Eric. 1990. How embryos work: a comparative view of diverse modes of cell fate specification. Development 108:365 389.

Davidson, Eric and Erwin, Douglas. 2010. An Integrated View of Precambrian Eumetazoan Evolution. Cold Spring Harb Symp Quant Biol 74:1-17.

Dawkins, Richard. 1982. Replicators and Vehicles. In Current Problems in Sociobiology, eds. Kings College Sociobiology Group. Cambridge: Cambridge University Press.

Endler, John. 1986. Natural Selection in the Wild. Princeton: Princeton University Press.

Felix, Anne-Marie. 1999. Evolution of Developmental Mechanisms in Nematodes. Journal of Experimental Zoology (Mol Dev Evol) 285:3-18.

Miklos, G.L.G. 1993. Emergence of organizational complexities during metazoan evolution: perspectives from molecular biology, palaeontology and neo-Darwinism. Mem. Ass. Australas. Palaeontols 15:7-41.

Nagy, Liza. 1998. Changing Patterns of Gene Regulation in the Evolution of Arthropod Morphology. American Zoologist 38:818-828.

Nelson, P. and Ross, M. 2003. Understanding the Cambrian Explosion by Estimating Ontogenetic Depth. [abstract] Developmental Biology 259:459-60.

Schierenberg, Einhard. 2001. Three sons of fortune: early embryogenesis, evolution and ecology of nematodes. BioEssays 23:841-847.

Schlichting, C.D. 2003. Origins of differentiation via phenotypic plasticity. Evolution & Development 5:98-105.

Thomson, Keith S. 1992. Macroevolution: The Morphological Problem. American Zoologist 32:106-112.

Wimsatt, William and Schank, Jeffery. 1988. Two constraints on the evolution of complex adaptations and the means for their avoidance. Pp. 231-273. In Nitecki, M.H. (ed.) Evolutionary Progress. Chicago: University of Chicago Press.

Wolpert, L. 1994. The evolutionary origin of development: cycles, patterning, privilege and continuity. Development [Supplement] 70:79-84.

Wolpert, L and Szathmáry, E. 2002. Evolution and the egg. Nature 420:745.

Wray, Gregory and McClay, David R. 1989. Molecular Heterochronies and Heterotopies in Early Echinoid Development. Evolution 43(4):803 813.


42 Comments

I'll wait for the next installment to continue the discussion.

Art,

Thanks for the clarification.

'Channeling Larry Moran' I assume means critiquing natural selection (NS). I've said elsewhere in this comment thread that other evolutionary processes may not be vulnerable to the same problems as NS, but "evolution" is too general an idea to analyze. One needs a specific and well-articulated causal process. In that respect, common descent via random mutation (RM) and NS is easily the best-understood, and modeled, theory in the field.

Thanks for the passages; both are interesting. In upcoming OD segments, I'll talk about the levels of selection question, which arises when the unit of selection moves from individual cell to colony to true multicellular organism. The postulate of some cells giving "up their lives for others," however, raises all sorts of questions for RM & NS.

"Heredity thus entails that at least one of four cells keep track of the instruction set for the lineage as a whole, if the cycle of differentiation is going to repeat (i.e., be maintained) in the next generation."

And it does appear that this is what happens.

"Alternative splicing has a crucial role in the generation of biological complexity, and its misregulation is often involved in human disease. Here we describe the assembly of a 'splicing code', which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons. The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences. Widespread regulatory strategies are revealed, including the use of unexpectedly large combinations of features, the establishment of low exon inclusion levels that are overcome by features in specific tissues, the appearance of features deeper into introns than previously appreciated, and the modulation of splice variant levels by transcript structure characteristics. The code detected a class of exons whose inclusion silences expression in adult tissues by activating nonsense-mediated messenger RNA decay, but whose exclusion promotes expression during embryogenesis. The code facilitates the discovery and detailed characterization of regulated alternative splicing events on a genome-wide scale."

http://www.psi.toronto.edu/wasp/

Paul,

"They" was intended to represent both "development" and "the evolution of developmental mechanisms".

I can foresee endless pedantic bickering about why I included "development" in my remark (blame it on my own attempts to cram as much of biology as possible into the simple cycle), so I'm happy to revise my comment so that we can focus on only the second noun.

I suspect, however, that after I diagram what you're saying, the same problems -- namely, needing to fix variants whose effects are invisible to selection -- will recur.

Ignoring the fact that you seem to be channeling Larry Moran (whose anticipated point in this regard is both correct and unremarkable), I don't see that in your illustrations or in my mental images.

A couple of quotes (unattributed for now):

"Reliability is the key demand made on development. This may be provided by apparent redundancy."

"We propose a scenario for the origin of the metazoa along the following lines. A mutation in a protozoan resulted in the failure of the cells to separate following cell division. In addition, a cytoplasmic bridge may have persisted. A colony could develop by the repeated binary division of the constituent cells. Such a mutation could thus lead to the formation of colonies which were loose aggregates. These colonies could fragment when large and so provide a means of reproduction. But what was the selective advantage?

It could have been increase in size, which could have provided protection against predatory cell, but much more likely is what may have happened when conditions became unfavourable. When food was in short supply there would have been insufficient resources for the individual cells to grow and multiply, and death was imminent. Now the virtues of multicellularity become evident. Some cells gave up their lives for others. That is they were "eaten" by their neighbours."

Paul,

I think you handled PZ's reply to you very well. It's well-worth remembering William Dembski's words about the "zero concession policy" of die-hard ID-critics:

Our critics have, in effect, adopted a zero-concession policy toward intelligent design. According to this policy, absolutely nothing is to be conceded to intelligent design and its proponents. It is therefore futile to hope for concessions from critics. This is especially difficult for novices to accept. A bright young novice to this debate comes along, makes an otherwise persuasive argument, and finds it immediately shot down. Substantive objections are bypassed. Irrelevancies are stressed. Tables are turned. Misrepresentations abound. One’s competence and expertise are belittled. The novice comes back, reframes the argument, clarifies key points, attempts to answer objections, and encounters the same treatment. The problem is not with the argument but with the context of discourse in which the argument is made. The solution, therefore, is to change the context of discourse.


Hardcore critics who’ve adopted a zero-concession policy toward intelligent design are still worth engaging, but we need to control the terms of engagement. Whenever I engage them, the farthest thing from my mind is to convert them, to win them over, to appeal to their good will, to make my cause seem reasonable in their eyes. We need to set wishful thinking firmly to one side. The point is not to induce a cognitive shift in our critics, but instead to clarify our arguments, to address weaknesses in our own position, to identify areas requiring further work and study, and, perhaps most significantly, to appeal to the undecided middle that is watching this debate and trying to sort through the issues.

You obviously were very civil to PZ in response, and you stuck to the scientific issues and responded to his objections, and clarified your position.

For the lurkers here who are open-minded, I think they are seeing that ID is about asking hard questions and making serious scientific investigations, while die-hard ID-critics are about brushing aside those tough questions through grossly inadequate responses, personal attacks, and unyielding misrepresentations (e.g. the "zero concession policy"). Good job.

Sincerely,

Casey

Art wrote:

Development (and the evolution of developmental mechanisms) does not interrupt the cycle (as you are implying in your illustrations), and they obviously are not predicated on some hypothetical starting point. Rather, multicellularity is a manifestation of specialization that is built around, or upon, the core cycle.

I'm wondering to which antecedent noun the bolded "they" refers here. Can you clarify, Art? Thanks.

I'll try to diagram (literally) your argument, Art, so I can follow it. Of course, it's arbitrary to pick the egg as the starting point for depicting development in animals, as we're really dealing with continuous cycles. I suspect, however, that after I diagram what you're saying, the same problems -- namely, needing to fix variants whose effects are invisible to selection -- will recur. There's a reason very good thinkers such as Wolpert have punted to hypothetical mechanisms such as the Baldwin effect, to do the work of building the first embryos. (Schlichting 2003 and Buss 1987 also wander off the neo-Darwinian playing field.)

At least one cell lineage, in the entire branching tree from the starting cell, must be capable of giving rise to another complete iteration of the tree.

Trying without a picture, because I am too lazy to make one or find just what I am wanting to describe:

Replace the tree metaphor with a more accurate one - a cycle whereby the organism undergoes a gametophytic and a sporophytic phase, onto which may (or may not) be assembled various and sundry developmental elaborations. This cycle could be either an unbroken totipotent lineage, several such lineages in the same organism, or lineages that undergo differentiation and de-differentiation. (Plants can do all of these.) Development (and the evolution of developmental mechanisms) does not interrupt the cycle (as you are implying in your illustrations), and they obviously are not predicated on some hypothetical starting point. Rather, multicellularity is a manifestation of specialization that is built around, or upon, the core cycle. And evolution is a process that can affect any part of the cycle. At any time in an evolutionary progression.

Scott,

You wrote:

Is the problem here how to get from egg to adult, or how to get from single cell to multi-cellularity, or how to get from a cell of one type to cells of multiple types back to a cell of one type that produces cells of multiple types?

Confusion arises because we're playing two games at once. One game is evolutionary: how did animals -- organisms that, in most cases, begin life as a single cell, a fertilized egg -- evolve from single-celled, or colonial, ancestors? [Btw, every egg is a single-celled organism, but the converse is not true.]


The second game is developmental: how many instructions have to be loaded into a starting node (cell) to specify n different terminal nodes (cells), with reproductive capability somewhere among the terminal nodes?

The games connect because an evolutionary process cannot win at the first game unless it simultaneously solves the second. Let's say some animal -- call it Bobby -- requires, minimally, 600 cells of 8 types to exist. Fewer cells, or fewer types: no critter.

And let's say the starting point for the evolution game is something like a choanoflagellate -- a single-celled eukaryote possessing many of the regulatory elements (genes and proteins) found in animals.

OK: Build Bobby from something like a choanoflagellate, using natural selection.

Hi Paul,

Thanks for responding. For now I'm just going to brainstorm a bit. If you don't have time to participate I'll understand, and I sure don't expect another response from you today.

Two common features of modern software development are inheritance and types. Types are typically usually represented through something called classes.

So it looks like I need to start with a ToyEgg and transform it into a ToyAdult, via a number of stages(with the difference being the Ontogenetic Depth) which is then capable of producing another ToyEgg.

But that doesn't seem quite right to me, as it seems to assume that the problem you're presenting has already been solved.

So I need to go all the way back to instruction 1 and (sort of) forget about "ToyAdult" for now.

IOW, our starting point is, ToyEgg == ToyAdult.

With an Ontogenetic Depth of 0 (no steps required to get from egg to adult-egg-maker).

Or am I just way off base here, confusing single celled organisms with an egg?

Is the problem here how to get from egg to adult, or how to get from single cell to multi-cellularity, or how to get from a cell of one type to cells of multiple types back to a cell of one type that produces cells of multiple types?

Or are they all the same problem?

just thinking. eek!

I humbly submit the following to all you learned scientists;
1. There is now available to the Scientific Community IRREFUTABLE proof that the FIRST CELL, consisting of at least several hundred protein molecules of greater complexity than 150 amino acids in length never could and NEVER DID happen at the start of the theoretical beginning of evolution. See 'Signature in the Cell' page 218.
2. Unless the scientific community can explain how 'mindless' evolution placed the "boundaries of infertility" between ALL the Species in the biological world, any further discussion on the THEORY of evolution is arguing in circles.
Read my book, second edition.
Sincerely, Kees van den Bosch, C.Eng.M.I.Prod.E., (Dip.B.I.A. Auck)

Scott,

At least one lineage must be capable of starting another iteration of the whole branching tree. I didn't consider meiotic reduction, or sex, because I wanted the simplest possible toy 'animal,' but of course one could add those features in a simulation.

Art,

You wrote:

I rather suspect that developmental biologists of many stripes would take you to task for exactly this claim

Why not you? You've taken me to task before: I'm listening.

At least one cell lineage, in the entire branching tree from the starting cell, must be capable of giving rise to another complete iteration of the tree.

I'm open to any suggestions for better phrasing, but any animal with terminal differentiation of cell types needs either (a) a dedicated totipotent lineage to provide gametes, or (b) some instruction to de-differentiate for the same purpose.

Um, yes.

So, apparently, you mean "One lineage retains the ability to execute all instructions".

I rather suspect that developmental biologists of many stripes would take you to task for exactly this claim, but that seems to be what you are intending in your cartoon.

Is this correct?

Hi Paul,

You did an excellent job of making this topic understandable. Hope to read more on this from you.

I'm wondering if I could build a simulation for your puzzle in software. I have a couple questions about the 'gamete'.

1. One lineage remembers all the instructions.

Do you mean one and only one, or at least one?

2. Is there always sex involved?

Does whichever lineage is carrying the instructions also have to know how to pass on only half the genetic material as it's contribution, or that assumed in your scenario?

Or is it even relevant?

Thanks

I posted this to PZ Myers science blog. Just in case it is rejected as a posting I'm posting it here as well. As a senior research scientist (BSc,Masters,Phd) it shames science to see the abuse Dr Nelson has been subjected to for simply putting forth a well-researched rational argument that has the temerity to rock the smug comfort-zone of materialistic-only-atheistic dogma.


PZ Myers states
"A bacterium in a sugar-rich environment vs. a bacterium in a sugar-poor environment will make long term changes in gene activity that can persist for a few generations using exactly the same mechanisms as an animal embryo sets up germ and somatic tissues;"

Doesnt this beg the question about how the information required in the DNA/RNA came into existence in the first place so that multi-cellular organisms could go through their complex development from egg to reproducing adult form. The animal embryo already contained this information to start with, bacteria did not now or ever have that information. How could they? Bacteria do not need that information and there is no selection pressure to accumulate and retain the genetic information that can produce some future multicelluar gamete-containing organism. Enter the conjectured environmental control in Wolpert. This is, if I understand correctly, the point of Dr Nelson's articles. BTW you have misrepresented what Dr Nelson quoted since he did specifcally mention "budding" in referencing Wolpert's paper. Also I find the personal attacks and ridicule (e.g. the graphic accompanying quotes from Dr Nelson) unjustified and repugnant. This type of intellectual bully-boy tactics simply act to damage your credibility as someone who is willing to hold a rational discussion that considers theoretical arguments and their empirical evidence in a way befitting the ideals of true science.

Art,

Please provide links to an online discussion that will illuminate why you think the adjectives "gametophytic" and "sporophytic" solve the problem of ontogenetic depth. Don't do this for my sake (I know what you're talking about), but for the ENV readers who may not know. I don't have time myself to explain the lingo and to try to reconstruct your (rather cryptic) point.

You wrote:

Obviously, Paul, there is a difference between carrying or remembering the instructions and executing each and every one of them. This is why Instruction 3 is so perplexing (and needless).

I'm open to any suggestions for better phrasing, but any animal with terminal differentiation of cell types needs either (a) a dedicated totipotent lineage to provide gametes, or (b) some instruction to de-differentiate for the same purpose.

But I welcome improvements to my instruction set!

Well, one more chain to trace, which we usually don't, is ofcourse, evolution of plants. As per Neo-Darwinism, all multicellular life forms evolved from a single accident(primeval soup etc), what theories do we have to explain the reproduction mechanisms present in plants? How did flowers, seeds and different plant types evolve? Is there any pattern that can connect the so many variations present in plants? If humans have evolved from Chimps based on variations in bones, skin, teeth and so on..), then how did for example, a coconut tree evolve? The reason to raise this question is to highlight the absurdity of information surrounding natural selection when we get into plants. This is especially true when we consider the evolution of limbs, scales, wings, bones and their extension as a basis for building theory of evolution. It is important to consider the evolution theory of plants, which is almost absent.

Hello Paul,
Good point about the explanation having a target- thanks.
Ontogenetic depth is not a hypothesis. Sorry for the confusion on that.
It does seem the 'distance' to be traversed will be traversed by DNA instruction. How many English instructions may or may not be similar to the number of DNA instructions. That is to say it is possible that number of the instructions that would be required by the English language are implemented by a single change in the DNA code.
This does seem to be an area that can be investigated by inspection-- how much change to the DNA of a single celled life form is needed to bring about multi-cellular forms?
Does anyone really know that?
(I'm guessing the answer will be 'many' which would be in your favor-no?)

Q: How many years will it take for a biological variation (anatomical, physiological, or behavioral) that depends on as little as 5 single nucleotide mutations to randomly arise?

please help? visit to answer:
http://darwinsparadox.blogspot.com/

"So why isn't every cell in C. elegans, or in you, a gamete?"

Let me turn the question around - if the gamete is the cell with the instructions (and apparently the only cell with them, if I am following you correctly), and if it is the presence of the instructions that determines the type of cell (that is what your question to me implies), then why aren't all gametes brain cells? And heart cells? And blood cells, etc., etc., etc.?

Obviously, Paul, there is a difference between carrying or remembering the instructions and executing each and every one of them. This is why Instruction 3 is so perplexing (and needless).

I'm afraid that this comment box isn't going to allow me to elaborate on my remark about the gametophytic-sporophytic cycle that governs all sexually-reproducing organisms. (Need pictures ...) I was sort of hoping that there would be enough familiarity to see what I was getting at. Oh well ...

Regarding Myers' response;

1) Myers began his response labeling Ontogenetic Depth as Nelson's "sciencey made-up term".

2) Myers asserts that Nelson's second essay is an exercise in demonstrating that Nelson does not understand basic biology. Filled with straw men and ad hominem as it is, Myers' response is an exercise in demonstrating that Myers lacks critical thinking skills, and lacking such skills, Myers' criticisms of Nelson lack credibility.

3) Myers writes;

Here's the gist of his [Nelson's] conceptual difficulty: he [Nelson] can't imagine how the first metazoan got from a crude colonial state [skip] to a state in which regions consistently specialized for specific functional roles, [skip] a mass of somatic cells that take care of feeding and motility, and a smaller mass of germ cells that do the job of reproduction.

So, according to Myers, Nelson's problem is that he cannot imagine things into existence. I suppose Myers means to imply that because Myers can imagine things into existence, and Nelson cannot, then that makes Myers the "sciencey" one.


Myers & Co. just make stuff up and pretend to be scientific.

Hi Sonic,

Natural selection does not have targets, but evolutionary explanation, employing the process of natural selection as a cause, certainly does. The targets of explanation for the origin of animals are (in part) the developmental trajectories we observe.

Ontogenetic depth is not a hypothesis. Think about the astronomical parallel in pt 1 of this blog series. The distance between the Earth and the Sun is what it is -- some measurable interval. One doesn't refute the distance to the Sun, as one would a scientific hypothesis that had made a failed prediction. But one can challenge the accuracy of a measurement.

Thanks for your suggestions, Matthew. I'll be posting a couple of entries about my ideas re making OD measurements more precise, and repeatable.

Hi Art,

So why isn't every cell in C. elegans, or in you, a gamete?

Please elaborate on your second comment; thanks.

Instruction 3 makes no sense to me. This is because all cells in the hypothetical lineage will remember all instructions.

Also, a better illustration that applies to all multicellular organisms is to picture things as a cycle of sporophytic and gametophytic stages, with further development being possible in either (or both) stages.

In terms of PZ's response to you, the only claims he made related to the subject of your posts is
as follows:

"Step one is simply cell adhesion. Step two is gene regulation. Step three is epigenetics. That's it."

Now that's attention to detail. No surprise though that most of his response dealt with accusing
you of quoting out of context - the opposition can get pretty worked up when their own views
are put under critical scrutiny.

The concept of Ontogenetic Depth (OD) is a good one.
Right now I'm thinking of it this way--
It seems one can build a latter that will take you to the roof top, but that same process will not get you to the moon.

It seems a weakness to the OD argument is that selection does not have to have a target- that is to say that it could be luck that creates a particular cell lineage- but cell lineages will be created (most will fail). In retrospect the one that ends up will seem likely impossible, but trial and error can account for that improbability.
Of course chance can account for anything if you want it to.

Another difficulty- the units of measurement will be translatable into snippets of genetic code. I'm not sure we know enough about how gene regulation works to know that a small change in a regulator couldn't bring about the types of changes you suggest are impossible.
The good news is this might be a means of testing the hypothesis.

Hi Bilbo,

Yes, I'll be replying. PZ's post was ludicrous. It appears he cited Wolpert's article without reading it.

To JLH,

Jeff Helix is right. My discussion treated ontogenetic depth as a problem for the process of natural selection. "Evolution" can mean many things, one of which is descent with modification via natural selection. Other evolutionary processes may exist, for which ontogenetic depth poses no difficulties.

I guess maybe I am pointing out the obvious, but whatever.

Nelson is elaborating on a hurdle that he holds selection cannot cross. Hence his use of the term "Natural Selection."

Hi Paul,

I was just wondering if you are planning on responding to PZ Myers' criticisms of your essays, including the accusation of quote-mining?

Paul,
Perhaps the best way to measure ontogenetic depth is by the number of types of binding events that must happen for an egg to develop into an adult.

By binding events, I'm referring to those specific interactions that control e.g., transcription, translation, phosphorylation, etc., such as protein/DNA binding, protein/protein binding, protein/RNA binding, etc. All these would depend upon specific interactions that are coded by genetic material (although not to ignore the 'epigenetic' effects).

I guess that number will be quite high, and we are probably a long way away from even an estimation. But in the end, it might be the only way to convince the skeptics that ontogenetic depth is a serious and meaningful concept that demands explanation.

Hi Anon,

What term do you use for the following?

[insert your term] is the distance in an animal species between the single-celled state and the adult phenotype capable of reproduction.

If you know a term from the biological literature naming this distance, pass it on. "Ontogenetic depth" names the distance, but does not specify units, for the reasons given in pt 1 of this blog series.

Distances, and units by which distances are measured (to give exact numerical values), are not the same thing, as the example of Earth-to-Sun distance in astronomy makes clear.

One of the advantages of evolution theory was the elegance of its simplicity --natural selection operating on random mutations. Now it looks like the evolutionary process itself is so complex that it was "intelligently designed" ---so we are back to the idea of ID.

Hi Bob,

Dictyostelium is a remarkable organism -- years ago, I read a great deal of J.T. Bonner's work dealing with it -- but I doubt its relevance to the problem of the origin of metazoan development. Wolpert (2002, 745) notes:

"There are multicellular organisms, such as the cellular slime molds, that develop by aggregation and not from an egg, but their patterns of cell behaviour have remained very simple for hundreds of millions of years. The evolution of more complex organisms increases the pressure to use an egg as a propagule."

Your attempt at "definition" of the onto genetic depth and analogy with the distance to the sun is a complete fail, it does not define anything.

I can define a "foot" as a length ofking's foot. After defining this length I can immediately measure king's, queen's or peasant's height, distance between cities and lot's of other things. I also know that distance to the sun is the same type of distance and I can imagine measuring it in feet even if I have no practical way of doing so.

On the other hand your definition of "ontogenetic depth" does not define anything at all. It is only a meaningless statement.

To be honest - I am not comfortable writing this for an adult - I would be comfortable explaining this to a third grader.

Paul,
Your use of "natural selection" as short-hand for the theory of evolution is confusing. You don't provide a clear justification for such usage and your arguments are not clear about whether you are addressing the process of natural selection or to the theory of evolution as a whole. Could you clarify? Thanks.

I'm not sure you need one lineage to remember all of the instructions - it's probably enough to know who your neighbours are (and in multicellular organisms, they're wildly signalling this).

You might want to look a the slime mould literature (before PZed drops a pile of papers on your desk) - there there's evidence of signalling and differentiation. There's even variation, but I don't know if it's enough for you.

That sure was a long read, would've fit nicely in "The Nature of Nature."

On second thought, that book is probably going to take me AT LEAST another month to plow
through, so maybe space constraints would've been an issue...

Never thought I'd have any respect for a young-earther, but you Paul seem to be a major
exception. I guess I just don't care what anyone personally interprets from a sacred text, so
long as that same text in question isn't used exclusively to draw a conclusion (and yes, that
standard applies to Ken Miller and Francis Collins as well for those of you who wish to take that out of context).

Now the waiting game begins for critics to tell you your explanation wasn't clear enough, and
demand that you try again.

Thanks, James -- we added figure labels. Sorry for the oversight.

First, the author referenced Figures 3 through 7. Yet, he failed to label any figures.

Nonetheless, by my count of the figures, Figure 8 is the one which describes Myers' "simplification" of the puzzle. The prose following Figure 8 describes how Myers explains his figure.

Actually, all Myers is doing is telling a little story. He is just making stuff up. What empirical data exists demonstrating his figure=storybook without input from an external intelligent agent?

After following this debate for a few years, I am convinced that no such data exists. All attempts to generate said data involve input from an intelligent agent to drive the desired storybook ending.

Myers has no solution to the puzzle. He only has religious faith in his belief that the puzzle is solved, and like someone from the stone age, he uses stories repeated over and over again to buttress his faith.

Science, on the other hand, requires repeatable empirical data and critical thinking to substantiate faith in a model of the physical world.

PZ Myers asked,

"He and Marcus Ross claimed to be doing actual work, measuring 'ontogenetic depth' in various organisms. How?"

Taking an average of cell divisions, from egg to adult cell, times number of cell types. Doesn't work -- far too crude a metric -- as I explained in Pt 1 of this blog series.

Anyone who tries will find that more accurate metrics become exceedingly complex very quickly.

As an engineer (retired) I have been asking the question of how evolution really works through the use of engineering analogies. It seems to me that evolution has to solve the same kinds of problems that an engineer has to solve when designing something new or changing an existing design.

I call it the problem of the three "P's". To build something the engineer has to concern himself with parts, plans, and process.

An overall plan has to be in place that controls a process that in turn directs where and when to place those parts to accomplish the overall design objective. Of course the plan also includes the design of all the parts and their spatial relationships.

Evolution as currently presented appears to be a "bottom up" process. Start with some parts, somehow throw them together, and sooner or later there is a morphologically different organism.

No engineer can approach a project that way and expect to keep his job.

This article with its discussion of ontogenetic depth suggests that evolution cannot expect to keep its job either.