Thursday, December 16, 2010

Wednesday, December 15, 2010

Canterbury Tales: Did Thomas Aquinas Deny the Immaculate Conception? (Garrigou-Lagrange)
Thomistica.net: Migne on-line. All of it.
VFR: The Darwinian theory of evolution is a fraud—and it’s not Lawrence Auster who says that, it’s the Darwinian scientists who say it

The Plausibility of Life. Resolving Darwin's Dilemma (Google Books)

An interview with Marc Kirschner and John Gerhart by Greg Ross

Can you describe the new theory briefly?


Our theory addresses the most mysterious part of Darwin's theory of evolution, namely "variation." As you may recall, he postulated that small differences of form and function inexorably arise among individuals in any group of animals. One individual, bearing its variation, may be more fit than others of the group to survive and reproduce in the environment at hand. In time, its descendants out-reproduce the others and come to replace them.


About half a century ago, we learned that heritable variation does not occur without mutation. Any place in the genome can suffer mutation, which is a change of the local DNA sequence. It appears to strike at random, and rarely. Our theory of "facilitated variation" is meant to explain how rare and random mutation can lead to exquisite changes of form and function.


We give center place to the fundamental processes by which animals develop from the egg to the adult and by which they function as adults. These are the "conserved core processes." They make and operate the animal, and surprisingly they are pretty much the same whether we scrutinize a jellyfish or a human. There are a few hundred kinds of processes, each involving tens of active components. Each component is encoded by a gene of the animal's genome, thus using up the majority of the 20,000 genes possessed by complex animals such as frogs, mice and humans.


The components and genes are largely the same in all animals. Almost every exquisite innovation that one examines in animals, such as an eye, hand or beak, is developed and operated by various of these conserved core processes and components. This is a profound realization for the question of variation, because it says that the different and seemingly novel features of animals are made and run by various of the same core processes, just used in different combinations, at different times and places in the animal, and used to different extents of their output. Variation is not as hard to get as one might initially think. A Lego analogy is applicable: The same Lego parts can be stuck together to give a model of the Eiffel Tower or of a soccer ball.


If the core processes remain the same, what changes in evolution? We suggest that it is the regulation of these processes. Regulatory components determine the combinations and amounts of core processes to be used in all the special traits of the animal. Whereas components of the core processes do not change in evolution, regulatory components do, and they are the targets of random mutational change. Genes for regulatory components comprise a minority of the genome (under a quarter, as a rough estimate), fewer than genes for core processes, but still a lot of genes and a lot of regulatory DNA. The thrust of our argument is that rather few mutational changes, affecting regulatory components, are needed to generate complex innovation.


In summary, then, we posit that the conserved core processes greatly facilitate the animal's generation of complex variation by reducing the number and kind of regulatory changes needed and hence the number of random mutational changes needed in the genome. Facilitation comes from the great versatility and adaptability of the processes and their proneness to regulation.


Where then do the conserved core processes come from? How were the Lego blocks invented?


In our book we dwell mostly on the long period of animal evolution from the onset of the Cambrian epoch, over 540 million years ago, to the present, during which altered regulation, due to random mutation, brought core processes together in various combinations and amounts, producing the enormous variety of new anatomical and physiological traits of the diverse animal groups.


The core processes had themselves evolved before the Cambrian, some even billions of years before. We envision four episodes, each separated from the next by a long interval during which life-forms diversified based on the varied use of those recently acquired processes, driven by regulatory change. First, as early bacteria-like cells evolved, the processes arose for synthetic and degradative (energy-producing) metabolism, for DNA synthesis and for gene expression, including protein synthesis. This innovation entailed the evolution of many hundreds of kinds of enzymes, proteins and genes that are found today in all life-forms—animals, plants, fungi, protists and bacteria.


The second episode occurred roughly two billion years ago, as the first eukaryotic cells evolved, perhaps coincident with the initial accumulation of oxygen in the atmosphere. Eukaryotic cells are much more complicated in their organization and coordination of activities. Processes evolved for arranging components at different places and for moving them from place to place. Genomes got larger, a complex cell cycle arose culminating in mitosis and cell division, and the first sexual reproduction took place with meiosis and the fusion of two cells. These new processes entailed the evolution of many new proteins, which seem to have originated from old proteins of bacteria. They are used by all modern life-forms except the bacteria and have been conserved with little change from those first eukaryotic ancestors.


A third episode occurred at the time of the earliest multicellular animals, perhaps one billion years ago. These processes of multicellularity involve the means of cell-to-cell communication, of cells adhering to each other and to a blanket of materials that cells deposit around themselves, and specialized junctions connecting cells. The means evolved for developing a multicellular animal from a single-celled egg. Specialized cell types evolved, such as nerve and muscle. Some of the new proteins used in these processes look as if they were spliced together from pre-existing parts, and their genes were spliced together from pieces of old genes, in various combinations and numbers. Others arose through the duplication of genes and diversification of base sequences of the duplicates, yielding large "families" of slightly different genes and encoded proteins.


A final episode, discussed in the book, occurred just before the Cambrian period and involved the innovation of the body plans of animals. This innovation compartmentalized the embryo and allowed a large increase in the complexity of development—namely, the independent use of different combinations and amounts of core processes in each of the domains of the developing animal's body plan, to give the many anatomical and physiological innovations of the Cambrian period to the present.


What are the recent advances that have permitted the new insights behind your theory?


Key recent advances have revealed how a single-celled egg develops to a functional adult. These advances rest on breakthroughs in many other areas of biology concerning how genetic information is transmitted to the next generation, how this information is recovered to produce the active components of cells, how energy is obtained and used, what limited set of chemical building blocks makes up all cells, how particular kinds of cells like nerves and muscles accomplish their functions, and on and on. Few of these insights were known even three decades ago. Much of this basic research was pursued without reference to evolution, but rather concerned what is required for life itself. The insights were surprisingly general, holding across large groups of animals, in cases even all life-forms from bacteria to humans.


The public knows about these breakthroughs mostly by their medical implications, but ultimately they allowed the understanding of development and evolution. Evolutionary biologists increasingly realized in recent decades that the changes of animals in evolution reflect changes in development. Now, in the past decade, the analysis of development has burst open. Out of all this research came the recognition of conserved core processes—what they do and what their components are. Out of developmental biology came the realization of the widespread use of these processes, and genome sequencing has shown that genes are widely conserved across the animal kingdom. For example, roughly 15 percent of our genes are like those of bacteria, 25 percent are like those of single-celled fungi, 50 percent are like those of fruit flies, and 70 percent are like those of frogs.


How can animals be so different and yet so much the same? The resolution of the paradox is found in the use of the same versatile adaptable components in different combinations and amounts to different ends, to generate the different anatomies and physiologies of the diverse kinds of animals.

And:
What questions remain to be answered?


The question is ongoing of what really occurs within the animal when it generates innovations. Our theory of facilitated variation is but a plausible sketch of how it might occur, and the theory reflects a direction in research, not a verdict reached.


Developmental biology is moving at a rapid pace, and the evolution of developmental mechanisms is a subject of high interest. For example, evolutionary biologists have long thought that the wings of birds are evolutionary modifications of the forelimbs of a reptile-like ancestor, which in turn are evolutionary modifications of the front fins of a lobe-fin fish-like ancestor. Now, every aspect of the development of fins, limbs and wings is under study to illuminate likenesses and differences down to the level of molecules and DNA sequences.


When a difference is found, the inquiry turns to the question: How different is it, really? What is new and what is old, at the level of molecules? What kinds of changes were needed to effect it? Similarly, the evolution of eyes is under intense study, as is the evolution of beaks of birds, or of segments, legs and wings of insects. Our main conclusion that evolutionary innovations involve very little that is really new, and that much innovation comes from the adaptive behavior of conserved processes, derives from these kinds of studies.


As a general direction in biology, the more we learn about how animals develop and function, the more we learn about how they have changed in evolution. While past variation will always be a subject for speculation and theory, the relevant research findings will increasingly clear our eyes and minds, and innovations will be produced in the laboratory, as is already under way to modest ends in agricultural animals. Presumably at that point, doubters would concede that maybe it's possible by natural causes.

The Authors:
Marc Kirschner
John Gerhart

Tuesday, December 14, 2010

Fr. Rhonheimer jumping to conclusions?

With respect to how he understands the "condom controversy":

Sandro Magister: On the Condom and AIDS, the Pope Has Come Down from the Cathedra
Usus Antiquior: A Theological Perspective on Church Music
Author: Nichols OP, Aidan

No explanation of why Fr. Alcuin Reid was replaced as editor; has his absence affected the quality of the journal and the number of subscriptions? I am among those who are boycotting...

Monday, December 13, 2010

A discussion of natural law

Constitutional Illusions
by Matthew O'Brien, November 15, 2010

The Particular Appeal of Universal Principles
Hadley Arkes, December 02, 2010
Responding to a review of his most recent book, Hadley Arkes asks some questions about the nature of natural law.

The Ambitions of Natural Law Ethics: A Reply to Arkes
Matthew O'Brien, December 03, 2010
What’s unnatural about the Kantian take on natural law.
William Carroll, Arsenic and the Meaning of Life

(via Godzdogz)