Are physics and chemistry sufficient to provide a basis for a theory of everything? The worldview of materialist naturalism that forms the foundation of NeoDarwinian evolution, Big Bang cosmogony, and molecular biology in general has been subjected to challenge for its monumental failure to explain life, consciousness and other mind-related aspects of reality. Two recent books, Why Evolution is True by Jerry Coyne [1], and Thomas Nagel’s Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature Is Almost Certainly False (...) [2], both authors being atheists, reflect the deep rift we find, not only in the religious conflict between creation and evolution, but in the fundamental awareness we all have that we are more than just molecular matter. This common sense understanding can only escape the notice of a particularly shallow ideological dogmatism that insists it has all the answers based solely on its unprecedented technological success. Science has come to represent two different things: (a) a body of knowledge, and (b) a method for acquiring knowledge. The problem arises when it is forgotten that there is no independent body of knowledge for science apart from its method – it keeps changing according to the results of the latest findings of the scientific method. The method is not to be abandoned because of those who would like to replace it with a fixed body of knowledge, which then becomes ideology. If biogenesis is hypothesized as the law of Nature, and we observe that life comes from pre-existing life in all our experience, while the hypothesis of abiogenesis, that life comes from matter, is never backed by any observation, then according to the scientific method—which one is to be accepted as true scientific knowledge? Obviously, the one backed by empirical observation. It is necessary to get free of ideological “knowledge,” and return to science as a method for gathering evidence that may lead to conclusions beyond the material naturalist view of Nature, and conforms to what we experience and rationally understand about the world in which we live. (shrink)

Origin of life studies have presented one of the most serious challenges to the mechanistic conception that life can be explained scientifically as a mere product of chemistry and physics. Hypotheses about the origin of life can be divided into two categories: (1) biogenesis – life comes from life, and (2) abiogenesis – life comes from non-living matter. The theory of the spontaneous generation of life from inanimate matter had been held even by the ancient Greeks and by numerous (...) scientists well into the 19th century. The theory of abiogenesis poses many problems for understanding the origin of life on Earth, and the appearance of life early in Earth’s history. Numerous chemical, mathematical and informational problems arise which make random mechanical processes of cellular formation and function unlikely. Fossil evidence contradicts a gradualist evolutionary mechanism of development of life, especially the well-known Cambrian explosion, in which highly developed metazoan species suddenly appear in the geological column without intermediate predecessors. But the physical conundrums that mechanistic theories of chemistry and physics face are only one side of the problem. Along with a rising chorus of philosophers, Thomas Nagel, an atheist philosopher, has protested that essential questions about the origin of life, and features such as mind, intelligence and morality are completely left unexplained by mechanistic evolutionary theories. In Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False, Nagel plainly lays out his argument that the modern materialist approach to life has conspicuously failed to explain something so integral to nature as mind or consciousness, thereby threatening to unravel the entire naturalistic world picture of biology, evolutionary theory and cosmology. [13] As an alternative he argues that at least natural teleological principles must be admitted to play a role in our view of science. He writes: “Each of our lives is a part of the lengthy process of the universe gradually waking up and becoming aware of itself.” The Vedantic view of the Absolute as sentient conceives of Bhagavan as the conscious and consequently personal source of the universe. This view holds that life is fundamental, and not merely coextensive with matter. It is thus consistent with the law of biogenesis which is scientifically established in agreement with empirical evidence. Life is the basis of Nature, not matter, and Nature is a system in which the different species are nodes or niches, each possessed of variety and adaptability. Evolution is of consciousness, not of the bodies of organisms. The sedimentary fossils are the result of catastrophic deposits, and are thus not indicative of gradual evolution which is concluded only on the questionable assumption of uniformitarianism. (shrink)

David Hume's famous riddle of induction implies a second problem related to the question of whether the laws and principles of nature might change in the course of time. Claims have been made that modern developments in physics and astrophysics corroborate the translational invariance of the laws of physics in time. However, the appearance of a new general principle of nature, which might not be derivable from the known laws of physics, or that might actually be a non-physical one (this (...) means completely independent of physical science) supports the notion that the course of nature can change in time. Here it is argued that natural selection satisfies the criteria that identify a general principle of nature which so far, appears to be non-derivable from the known laws of physics and therefore, it is likely that it arose in the course of time, thus leaving open again the quest for a true solution to Hume's second problem. (shrink)

It is not that scientists make an hypothesis first, and then try to find the data to fit that hypothesis. Rather, the process is first observation, then an hypothes is made to describe the data, then conclude that the data has been described by the hypothesis. But this is not an explanation of the phenomenon. It is merely a description of the data in different terms, usually mathematics. It is essentially a tautology. Thus to observe various points and connect them (...) by a line or curve, then to find the mathematical formula that will construct that curve is said to be the law of the curve or the law governing the data points. If those data points happen to be the positions of a planet in space at different times, then the mathematical equation that produces the points on that curve is called the law of motion of the planets. Now, in origin of life studies, observation reveals that life comes from life only. There is no evidence whatsoever to indicate that life is produced out of non-living matter. It was Louis Pasteur who disproved this theory of abiogenesis. From a purely empirical viewpoint, therefore, we have no justification for stating that life comes from inanimate matter. The evidence is that throughout the entire history of modern science such a production of life from matter has never been observed. The question is: Why make a hypothesis about something that has never been observed? If we want to be scientific, then our hypothesis must match the data. Life comes from life is observed all over the Earth, and we might say, all over the universe as far as we have observed it. So where is the justification for claiming otherwise? Rather, we must conclude that the claim that life comes from matter is completely unscientific because it is not a conclusion based on any empirical observation at all. It is purely wishful thinking — a “naturalistic” or materialistic ideology that is masquerading as science. It is thus doubly deceitful since it is not only an unproven belief but an ideology that poses as a scientific theory. (shrink)

“Indeed, we now know that the proportion of genetic sequences on earth that belongs to visible organisms is negligible. Furthermore, only 15% of the genetic sequences found in the samples from the environment and from feces analyzed in metagenomic studies belong to the three domains of microbes currently recognized in the tree-of-life framework – bacteria, archaea, and eukaryotes. Viruses contain another 15-30% of these genetic sequences.” This means that the majority of unidentified genetic sequences pose an unresolved problem. Where do (...) they come from? New genes suddenly appear, called ORFans (“orphan genes”) without any precursors. They may be produced by gene duplication, or fusion, or some other unknown process. Yet, Darwin’s tree of life concept would make it impossible to consider such processes. The transfer of genetic sequences from parasites to hosts could involve hundreds of genes for bacteria or viruses. But, as Raoult writes, “the current classification of the domains of life is based on the ribosome – the production apparatus of proteins – which does not exist in these viruses.” Adherence to the dogmatism of Darwin thus prevents these new discoveries, that overturn his century-and-a-half old teachings, from ever reaching the new generation of scientists. Raoult concludes, "Genetic research, in particular, must be free to find new models to explain, and enhance, twenty-first-century scientific discovery. Today, Darwin’s theory of evolution is more a hindrance than a help, because it has become a quasi-theological creed that is preventing the benefits of improved research from being fully realized.". (shrink)

The analytical understanding cannot deal with integral wholes and therefore cannot understand the soul or God. The material body is illusory in the sense that it cannot be understood in its true identity without knowing its relationship to God. Analyzing its composition in terms of separated molecules or neurons is also illusory. To understand how to go from an untrue or partially true part to its truth in the whole a method developed by Hegel called conceptual thinking is required. Reproduction (...) is not merely concerned with individuals, it involves the genus or genus process. The universal that determines the species is not changed when particulars under the universal change, die, reproduce according to their “own kind” or species. Without connecting the individual organisms with their species we may wrongly think they can evolve into any species by chance. But this is not how individual and species are related to each other. The species determines how the individuals will appear and controls their reproduction, growth, and so on. They are not independent to become what they want by choice or by chance. Everyone calls themselves “I” so “I” is a universal, although each means only oneself. In the same way each organism is identified with its species, although we mean its own particular organism – for example, a dog and not canine in general. Thus the universal and particular cannot be separated from each other. Similarly individuals who identify only personal reason independent of universal Reason are misconceiving their true identity. At the same time universal and particular are related, they are not the same but a unity in difference. The universal by itself is as abstract as the particular by itself. At the same time their relation can only be comprehended within a higher unity, the higher Self or Supreme Individual. (shrink)

Gregor Mendel (1822-1884) was the first to explain that certain 'traits' were inherited in plants from one generation to the next. These would later become known as genes. Frederich Miescher in 1869 analyzed a substance from the nucleus of cells, which he therefore called nuclein. Further study of nuclein revealed that it contained elements like hydrogen, oxygen, nitrogen and phosphorous, with a specific ratio of nitrogen to phosphorous. Then in 1878 Albrecht Kossel determined that nuclein contained nucleic acid, from which (...) he isolated five nucleobases (nitrogen compounds now referred to by the letters C, G, A, T, U representing cytosine, guanine, adenine, thymine, and uracil). It was also discovered that ribose, a sugar was present in the nuclein compound. What Miescher had isolated from the cell nucleus was actually what would latter be identified as DNA (Deoxyribonucleic acid). C. H. Waddington (1905 - 1975) first proposed the term “epigenetics” in 1942 to describe the region between the gene and the whole organism (phenotype) [3]. Today, what is called the epigenome refers to all the chromosomal modifications, DNA modifications, chromatin protein modifications and their complexes. It is the epigenome that determines both the expression of the genes and their inheritance. R. A. Jorgenson reports [4], "Many of these modifications appear to be “programmable” and to be “read out” to influence chromosomal functions." Nobel laureate Barbara McClintock stated this revolutionary proposal more clearly in her Nobel lecture [5], “to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a ‘thoughtful’ manner when challenged.” In 1960 R. A. Brinks suggested that chromosomes possess a paragenetic function in addition to their genetic function [7]. The physical nature of the paragenetic function is characterized by the variety of forms or states of chromatin that can reside at any genetic locus. While the genetic function is stable, the paragenetic function is labile and programmable in ontogeny. It is this latter function that allows organisms to transfer informational macromolecules (RNA and proteins) in a systematic and regulated manner over what is known as the “RNA information superhighway.” Given this capacity, organisms may be able to store information at numerous genetic loci in the form of paragenetic chromatin states, which can be reprogrammed during ontogeny or environmental stress [8]. This reprogrammable system could operate over the whole organism as a storage device, allowing it to make informed ‘decisions' during growth and development, or in response to the environment. Such processing capacity could be considered a form of ‘intelligence,' which also could be passed on to future generations. The study of the flow of information within and between cells and organisms represents the cutting edge of modern biological research. While physical correlates of cognitive behavior in living organisms are being discovered, it does not spell reduction to such correlates. The electronic activity within the physical components of a radio, for example, may be minutely determined, but ultimately it is not merely the electrical activity that produces the intelligent speech that is heard. Only the intelligent person whose voice is being broadcast through the radio can explain that. Without the broadcaster, the radio would sit silently even though fully functional. An organism without its living agency also appears to be devoid of metabolic activity although all the chemical components are fully present. How to connect life to matter will be the ultimate challenge that has to be met. This will prove to be a philosophical problem we hope to address in the near future. (shrink)

All the central assumptions of the Modern Synthesis (Neo-Darwinism) have been disproven. [1, 2] An article with the title, "Rocking the foundations of molecular genetics,” appearing in the prestigious Proceedings of the National Academy of Sciences at the end of 2012 [3] would have not been possible a decade ago. Groundbreaking experimental evidence of epigenetic maternal inheritance over several generations was published in the same journal, throwing the whole foundation of 21st century molecular genetics into question. Neo-Darwinism attributed genetic change (...) to random events, in which physiology was assumed to play little role. "The germ line was thought to be isolated from any influence by the rest of the organism and its response to the environment. [3] The fundamental concepts that constitute the foundations of contemporary systems biology include holism, emergentism, and robustness, compared to the concepts of reductionism, mechanism, and homeostasis, that form the foundations of molecular biology. [18] Holism is to be contrasted with reductionism which considers a system as merely composed of a sum of parts. Emergentism, the appearance of hierarchical levels of organization, is contrasted with mechanism of independent linear events. Robustness refers to the preservation of the functionality of a system to a certain degree despite external or internal changes, while homeostasis refers to maintaining the stability of the state of a system. The Vedantic view also proposes viewing life from the Organic Whole perspective, in which consciousness forms the supporting basis. The conscious agent is an important part of that view, but the absolute conception of a unifying center is not to be omitted if a proper conception is to be achieved. (shrink)

The neo-Darwinian theory of genetic random mutation and Natural Selection, does nothing to explain speciation. Thus, what has been called "natural selection" has come under much scrutiny and critique in recent times. The problem is that natural selection requires the existence of a stable array of species from which selection can be made. So natural selection does not perform the speciation, only the selection after speciation has occurred. The activity of creating new species must therefore lie in the random mutations (...) of the genome. But this raises the problem that such mutations are generally always fatal to the organism, plus a whole host of other problems that modern advances in molecular biology have revealed about the detailed mechanisms occurring in DNA replication processes, including such things as intrinsic error correcting mechanisms during DNA transcription. Thus a theory of how species arise (speciation) does not currently exist in biology. The Vedantic/Bhagavat paradigm rejects the objectivist theory of evolution as not only wrong but an impediment to the actual scientific comprehension of Nature. The Vedantic conception of Life is a fully differentiated/determinate one that displays its variety in and as an dynamic organic whole. The crucial element of interdependence that is missing in modern theories of insular organism life is fully embraced in what we may call the Post-Darwinian, post-reductionist, post-modern conception of Life the Vedantic/Bhagavat conception offers. (shrink)

The first hint of how to begin our inquiry is given in the second aphorism of Vedanta-sutra. Janmadasya yatah. Janma means birth, and asya refers to all that has been created from Brahman or the original source - which is spirit. Brahman means Spirit or God. It is not a matter of merely knowing what is immediately present before us. We want to know where it all comes from. This is actually very practical if we want to properly understand anything. (...) For example, let us say an aboriginal villager enters a city for the first time in his life and sees numerous skyscraper buildings. He may think these buildings to be natural features of the environment, just like the caves in his mountain village. Thus, in order to properly understand what a building is, not only its present appearance but how it got there, or where it came from is necessary. Only then can one say that he has properly understood what a building is. Likewise, scientists are not merely interested in observing the world, they want to understand what is beyond its immediate appearance, and comprehend what principle constituents it comes from - what has made or caused it to be what we observe. This is what we mean by scientific understanding. (shrink)