From Stephen C. Meyers book : Darwins doubt :
Starting in the autumn of 1979, at the European Molecular Biology Laboratory in Heidelberg, two venturesome young geneticists, Christiane Nüsslein-Volhard and Eric Wieschaus , generated thousands of mutations to investigate the genomes of tens of thousands of fruit flies (species: Drosophila melanogaster). They hoped to get them to divulge the secrets of embryological development. In technical jargon, Nüsslein-Volhard and Wieschaus performed "saturation mutagenesis" experiments. After feeding male flies the potent mutation-causing chemical (i.e., mutagen) ethyl methane sulphonate (EMS), Nüsslein-Volhard and Wieschaus bred the males with virgin females. They then examined the offspring larvae for visible defects.
Wieschaus responded more soberly, wondering aloud about whether his collection of mutants offered any insights into how the evolutionary process could have constructed novel body plans. "The problem is, we think we've hit all the genes required to specify the body plan of Drosophila," he said, "and yet these results are obviously not promising as raw materials for macroevolution. The next question then, I guess, is what are—or what would be—the right mutations for major evolutionary change? And we don't know the answer to that." Thirty years later, developmental and evolutionary biologists still don't know the answer to that question. At the same time, mutagenesis experiments—on fruit flies as well as on other organisms such as nematodes (roundworms), mice, frogs, and sea urchins—have raised troubling questions about the role of mutations in the origin of animal body plans. If mutating the genes that regulate body- plan construction destroy animal forms as they develop from an embryonic state, then how do
mutations and selection build animal body plans in the first place?
To build a new animal and establish its body plan, proteins need to be organized into higher- level structures. In other words, once new proteins arise, something must arrange them to play their parts in distinctive cell types. These distinctive cell types must, in turn, be organized to form distinctive tissues, organs, and body plans. This process of organization occurs during embryological development. Thus, to explain how animals are actually built from smaller protein components, scientists must understand the process of embryological development
THE ROLE OF GENES AND PROTEINS IN ANIMAL DEVELOPMENT
As much as any other subdiscipline of biology, developmental biology has raised disquieting questions for neo-Darwinism. Developmental biology describes the processes, called ontogeny, by which embryos develop into mature organisms. Within the past three decades the field has dramatically advanced our understanding of how body plans arise during ontogeny. Much of this new knowledge has come from studying so-called model systems—organisms that biologists can easily mutate in the lab, such as the fruit fly Drosophila and the nematode Caenorhabditis elegans. Although the exact details of animal development can vary in bewildering ways depending on the species, all animal development exemplifies a common imperative: start with one cell, end with many different cells. In most animal species, development begins with the fertilized egg. Once the egg divides into its daughter cells, becoming an embryo, the organism begins heading toward a well- defined target, namely, an adult form that can reproduce. Arriving at that distant target requires the embryo to produce many specialized cell types, in the correct positions and at the right time. Cell differentiation involves coordinating the expression of specific genes in space and time, as the number of cells, taking on their different roles, rises from one to two to four to eight, doubling and doubling until it reaches thousands, millions, and even trillions, depending on the species. The number of cell divisions and the total number of cells reflects the number of different cell types the adult needs. This in turn requires producing different proteins for different cell types. For example, the specialized digestive proteins that service the cells lining the adult intestine differ from proteins expressed in a neuron found in the nerve tract of a limb. They must differ because each performs dramatically different functions. So, during development, the appropriate genes must be turned on, or "up-regulated," and turned off, or "down-regulated," to ensure the production of the correct protein products at the right time and in the right cell types.
Specific proteins play active roles in regulating the expression of genes for building other proteins. The protein actors playing these coordinating roles are known as transcriptional regulators (TRs) or transcription factors (TFs). TRs (or TFs) usually bind directly to specific sites in DNA, either preventing (repressing) or enabling (activating) the transcription of specific genes into RNA. TRs or TFs convey instructions about which genes to turn on or turn off. Their three-dimensional geometries exhibit characteristic DNA-binding features, including a specific domain of 61 amino acids that wraps around the DNA double helix. Other transcription factors include the zinc finger and leucine zipper motifs that also bind to DNA. Transcriptional regulators and factors are themselves controlled by complex circuits and signals transmitted by other genes and proteins, the overall complexity and precision of which is breathtaking.
Painstaking genetic research—performed by Nüsslein-Volhard and Wieschaus and many other developmental biologists—has uncovered many of the key embryonic regulatory genes that help switch cells into their differentiated adult types. This research also uncovered a profound difficulty cutting to the very core of the neo-Darwinian view of life.