Genes in Action — Mystery Link:
From genetic information to cell structure and function
The point of WindowView perspective building is to stop ourselves to pause, to ask the questions that are obviously too often quickly swept aside. For example, a cell operates many functions based on enzyme activities. One operation, say moving some DNA from one location to another location on the same or other chromosome, requires a bit of coordinated activity. It happens, that's a fact. That it happens by several coordinated steps, by several enzymes is amazing. To plan to move from house to house takes anticipation of multiple tasks. You can think ahead of how the move will happen. But does a cell think? Might evolution in advance of the existence of a cell 'know' to develop just the correct three or so enzymes to anticipate the need to move DNA around? Furthermore, that a cell has any ability to anticipate the need to move DNA goes beyond chance. Science simply reports that the steps take place. But when do we get the opportunity to be 'blown away' by the wonder of it all. Genes move about the genetic house (i.e., within a cell's nucleus). This isn't merely happenstance... it creates powerful adjustments to meet demands from outside the cell. The way genes work exhibits an informational system that is incredible. Think about it! Mechanistic explanations are not enough to account for the systems that make us work—indeed they work in marvelous fashion. Yet the scientific journal reports are expressionless—lacking wonder, lacking critical thinking.
Recombination is not a simple process. We do not yet understand how the breaking of chromosomes and the swapping of pieces is done as precisely at is it is. We do know, though, that it is controlled by special enzymes that break the chromosomes, exchange the pieces, and rejoin the free ends. Spetner (NBC) Page 39
Geneticists have found that the inversions, deletions, insertions, and transpositions are not just haphazard events. Special pieces of DNA that jump around in the chromosomes cause these genetic changes. Short pieces of DNA, called transposons, have been found to jump from place to place in the chromosomes. They have also been found to activate other special, shorter, pieces and make them jump as well. Spetner (NBC) Page 42
A. transposon has in it sections of DNA that encode to of the enzymes in it needs to carry out its job.
But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and as well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learned what it really does. If the source of the variation for evolution were point mutations, we could say the variation is random. But if the source of the variation is the complex process of transposition, and then there is no justification for saying that evolution is based on random events. I'll return to this subject in Chapter 5 and again in Chapter 7. Spetner (NBC) Page 44
Neo-Darwinism is elegantly simple. The theory can be summarized in four propositions: every organism develops according to a program encoded in its genes (which is to say, its DNA); DNA is the hereditary material that transmits traits from organisms to their descendants; new traits occasionally arise because of DNA mutations; and natural selection produces both microevolution (within a species or genus) and macroevolution (above the species or genus level) by favoring advantageous traits and thereby increasing the frequency of their genes in the population. Wells (MC) Page 51
The modern synthesis of Darwin's theory with population and molecular genetics, however, left out embryology. Embryology was "second to none in importance" for Darwin, and along with homology provided him with such convincing evidence for descent with modification that he would have adopted this theory "even if it were unsupported by other facts or arguments" (Darwin 1936, 346, 352). Yet embryology was virtually ignored by the modern synthesis (Bowler 1989; Gilbert 1994; Sapp 1987). Wells (MC) Page 52
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Darwin had noted that vertebrate embryos resemble each other at a certain stage in their development and considered this resemblance to be evidence of common ancestry. In fact, however, in the early stages of their development vertebrate embryos are radically different from each other. In the 1980s comparative embryologists began to find many cases in which organisms with very similar morphologies follow radically dissimilar pathways in early development. Rather than regarding this as a threat to Darwin's theory, evolutionary biologists are now interpreting it as evidence that early development can be easily modified to produce macroevolutionary change.
Thus developmental genetics seems to have provided empirical confirmation of the neo-Darwinian proposition that organisms develop according to a program encoded in their DNA that evolved from a common ancestor through mutation and natural selection. And comparative embryology seems to have provided evidence that major changes in the early development are relatively easy to achieve. According to a recent review of the advances in evolutionary and developmental biology, "the evidence for evolution is better than ever" (Gilbert, Opitz, and Raff 1996, 368).
Or is it? In the opinion of some biologists, myself included, recent discoveries in developmental genetics and comparative embryology pose serious problems for neo-Darwinism. Those discoveries have been welcomed into the City of Darwin, but I predict that, like a Trojan horse, they will bring that city down. To illustrate my point I will survey recent data about homeotic genes, which neo-Darwinists consider to be their best evidence that evolution modifies development by altering genetic programs, and show that those data raise more questions than they answer. Wells (MC) Page 52
It seems as though the neo-Darwinian proposition that "novel morphological forms in animal evolution result from changes in genetically encoded programs of developmental regulation" (Davidson, Peterson and Cameron 1995, 1319) has been empirically confirmed.
Or has it? Although most Darwinian biologists have not yet realized it, the very universality of homeotic genes invalidates the grand claims that are made for them. Here is why: if biological structures are determined by their genes, then different structures must be determined by different genes. If the same gene can "determine" structures as radically different as a fruit fly's leg and a mouse's brain or and insect's eyes and the eyes of humans and squids, then that gene is not determining a much of anything.Wells (MC) Page 56
Similarly, except for telling us how an embryo directs its cells into one of several built-in developmental pathways, homeotic genes tell us nothing about how biological structures are formed.
In other words, the universality of homeotic genes is supposed to be due to their presence in a common ancestor, but the preponderance of the evidence suggests that the common ancestor lacked the features that those homeotic genes now supposedly control. From a Darwinian perspective this is a serious problem. According to neo-Darwinism, complex gene sequences gradually evolve by conferring selective advantages on the organisms that possess them. The gene sequences confer selective advantages only if they program the development of useful adaptations. If a primitive animal possessed homeotic genes but lacked all the adaptations now associated with them, then those genes must have originated prior to those adaptations. How then did homeotic genes evolve? Wells (MC) Page 57
The bottom line is that each new piece of evidence demonstrating the universality of homeotic genes (and thus their independence from any particular adaptation) makes their presence in a putative common ancestor more difficult for neo-Darwinists to explain. Ironically the very discoveries that Darwinian biologists now find so exciting are adding to the list of the difficulties for their theory.
If, instead, homeotic genes are the product of intelligent design, this particular difficulty disappears. Once design is admitted, there is no obstacle to saying that a complex gene sequence can originate quickly, based upon future rather than past usefulness, and that its designer can incorporate it into a wide variety of organisms that otherwise share few structural similarities. Just as an engineer would not be surprised to find similar ignition switch is in different kinds of vehicles produced by the same of manufacturer, so biologist who it meant design need not be surprised to find similar homeotic genes in most all or all types of animals.
Thus a design approach is better able than a neo-Darwinism to accommodate a recent discoveries in developmental genetics. The superiority of a design perspective is also apparent in the light of recent discoveries in a comparative embryology. Wells (MC) Page 58
Genetic Programs Or Organic Forms?
[We assume and DNA explains it all; but not so! ]
Although molecular biology has demonstrated conclusively that DNA carries the genetic code for the amino acid sequence of proteins, this is not sufficient to specify a whole organism. Combining DNA with all the ingredients necessary for protein synthesis does not make a cell.
Why not? Consider the analogy of building a house. One needs to specify a and provide the building materials: boards of particular sizes and shapes, nails, insulation, shingles, windows, doors, electrical wires, pipes and so on. One also needs to specify the order in which components should be assembled, because the foundation must be completed before the walls and roof are erected and the plumbing and wiring are installed. Most important, one needs to specify the intended floor plan, because the individual materials could be combined in a number of different ways. Molecular biology has shown that an organism's DNA specifies the building materials. It turns out, however, that the assembly instructions are largely in other components of the cell, and that the floor plan has not yet been discovered. Wells (MC) Page 62
... but the three-dimensional structure of large aggregates of these building blocks is not determined by the structure of individual submits anymore than the floor plan of the House is determined by the shape of its bricks.
Consider, for example, the cytoskeleton ...
... assembly of these subunits into a three-dimensional structures is a dynamic process which depends on intracellular nucleating sites and environmental cues, ...
Thus of the generation of shape, or morphogenesis, is not reducible to subunit structure. Developmental biologist Brian Goodwin writes that "genes are responsible for determining which molecules an organism can produce" but this fails to address the basic problem posed by morphogenesis, namely, how distinctive and spatial order are arises in embryos." He concludes that "the molecular composition of organisms does not, in general, determine their form" (Goodwin 1985, 32).
Shape is not the only variable unspecified by the DNA. In multicellular organisms, cell types differ in physiology as well as morphology.
For example, liver cells, muscle cells and nerve cells are not only shaped differently but also manufacture different proteins and perform very different biochemical functions. Yet they all contain the same DNA, which they inherited from the fertilized egg.
Whatever is producing the differences, it must be something other than their DNA. Developmental biologist H. F. Nijhout writes that "the only strictly correct view of the function of genes is that they supply cells, and ultimately organisms, with a chemical materials." Furthermore the function of the homeotic and other regulatory genes "is ultimately no different from that of structural genes, in that they simply provide efficient ways of ensuring that the required materials are supplied at the right time and place" (Nijhout 1990, 444).
...there it is evidence that cell differentiation is due to factors that are regionally localized in the fertilized egg. But such regional localization precedes gene activity in the cells whose developmental pathways it determines. Wells (MC) Page 63
In other words, even in those organisms in which cellular differences can be traced directly to regional differences in the fertilized egg, the floor plan is independent of the DNA.
If the organism's floor plan is not in its DNA, where is it? Other features of an embryo that can carry developmental information include the cytoskeleton, the membrane and the cytoplasm. When a sperm and fertilizes an egg, in many cases it transmits not only DNA but also a nucleating center, or centrosome, for the embryonic cytoskeleton. Wells (MC) Page 64
Experiments with vertebrate tissues show that dividing cells transmit cytoskeletal patterns to their descendants that determine the spatial orientation of cells in those tissues (Locke 1990).
Membranes also carry morphogenetic information that can be inherited independently of DNA. Biological membranes are not merely featureless bags but included proteins and other molecules that are spatially distributed in highly structured patterns; and when a cell divides, its progeny inherent not only its DNA but also a membrane pattern. Experiments with protozoa (single-celled organisms possessing nuclei) show that surgical modifications of the membrane pattern can be passed on for many generations even though the organism's DNA has not been altered (Nanny 1983; Nelson, Frankel, and Jenkins 1989). Wells (MC) Page 64
So there are clearly other factors involved in heredity and development besides DNA. By itself this observation would not require the formulation of a radically new theory of evolution. Although it is incompatible with reductionistic, DNA-based neo-Darwinism, it is not necessarily incompatible with the more general notion of descent with modification. Biologist Sydney Brenner, who originally coined the term "genetic program," then later repudiated it for being too simplistic, did not abandon his commitment to Darwinian evolution, much less its underlying naturalism (Brenner 1973; Lewin 1984). Wells (MC) Page 64
It seems unlikely that such patterns could determine the final outcome of embryogenesis without noticeably affecting the intervening stages. Yet similar sea urchins can exhibit remarkable differences in cell fate determination during early development.
If an organism were a house, its DNA would specify the building materials, and the inherited arrangement of its cytoskeleton, membrane and cytoplasm would help to specify the order in which those materials are assembled. But the floor plan is determined neither by the building materials nor by the order in which they are assembled. Where then is the floor plan of the organism?
Some as-yet-undiscovered law of development may do for embryos what quantum mechanics does for atoms and molecules.
A vague hint of what is to come might be found in complexity theory, in which physicists use the term attractor to describe stable points, curves or surfaces toward which complex movements tend to gravitate. Wells (MC) Page 65
[ See pendulum example ]
The sort of thinking that could account for recent discoveries in comparative embryology and open the way to future progress in biology is alien to neo-Darwinism. Instead creative thinking is much more likely to flourish in an intellectual environment in which organisms are regarded as designed. If an organism is designed, then the idea for it preceded its existence, and formal and final causes are real. To be sure, one can regard organisms as designed and still try to treat them as molecules in motion; but one is also liberated, even encouraged, to regard them as much more. Wells (MC) Page 66
Conclusion: toward a new paradigm
According to Thomas Kuhn, science normally functions within a "paradigm," a general theory that has successfully answered some important questions and that lays out a research program for further investigation (Kuhn 1970). Typically the general theory integrates specific inferences from various scientific disciplines and includes philosophical assumptions as well. Thus the Ptolemaic paradigm that dominated Western science until the sixteenth century integrated not only medieval astronomy but also Aristotelian physics and a geocentric cosmology. Wells (MC) Page 66
Neo-Darwinism integrates data and inferences from a variety of scientific disciplines; it incorporates philosophical assumptions (such as naturalism); and its research program currently guides the work of most biologists. If Kuhn was correct, we may expect to see Darwinian biologists, like Ptolemaic astronomers, dealing with anomalous evidence by adding epicycles to their theory.
Anomalous evidence From developmental biology has been accumulating at an accelerating rate since 1980. The anomalies are not isolated results reported in obscure publications; instead they have been reproduced in many reputable laboratories and reported in the best peer-reviewed journals. In their zeal to confirm neo-Darwinism, some of the most talented biologists in the world have devoted years of work to analyzing the developmental effects of homeotic genes or searching for them in every conceivable type of organism. Each new discovery is featured prominently in the scientific press and celebrated as another nail in the coffin of those who oppose Darwinism. Ironically however, these new discoveries about homeotic genes are subverting the paradigm that inspired them, because as those genes turn out to be more and more universal, the control they exercise in development of turns out to be less and less specific and their origin more and more difficult to explain from a Darwinian perspective. Neo-Darwinists are left with ad hoc speculations about how homeotic gene sequences might have evolved before the adaptations which they now control; but these are merely the epicycles of a dying paradigm. Wells (MC) Page 67
The new paradigm, it seems to me, will be based on design. A design paradigm can account far better than naturalistic Darwinism for the origin of complex genes and their presence in a wide variety of organisms. A design paradigm can nurture this sort of formal and teleological thinking that will enable biologists to discover the laws of development that have so far eluded them. In order for a design paradigm to out-compete Darwinism, however, it will have to be developed to the point where it is philosophically rigorous and scientifically fruitful. I am confident that this can be done and that this conference will be a giant step in that direction. Wells (MC) Page 68
Writer / Editor: Dr. T. Peterson, Director, WindowView.org
Quotations from "Mere Creation" (MC) edited by William A. Dembski are used by permission of InterVarsity Press, P.O. Box 1400, Downers Grove, IL 60515. www.ivpress.com All rights reserved. No portion of this material may be used without permission from InterVarsity Press.