Sunday, November 24, 2013

Fred Sanger, Protein Sequences and Evolution Versus Science

Are Proteins Random?

The passing of the great biochemist Frederick Sanger this week reminds us of another one of evolution’s many scientific failures, namely the view that protein sequences are random. Here is how one obituary explains it:

… Chibnall and Sanger believed that there might be a real possibility of determining the exact chemical structure of proteins. This idea was controversial at the time as, although the 20 or so amino acids that can go to make up proteins were known, most scientists believed the arrangement of different amino acids in a protein to be random. One professor had even produced a complex mathematical formula that would express this random function. Thus, when Chibnall tried to get Sanger a grant from the Medical Research Council to work on protein structure, the grant was refused because “everyone knew” that the pattern of amino acids in a protein was random.

Nevertheless, Sanger scraped together enough money from various sources to start work. From 1944 to 1951 he held a Beit Memorial Fellowship for Medical Research; and in 1951, by which time the Medical Research Council had come to recognise the importance of his work, he became a member of the MRC’s external staff.

The protein which Sanger chose for his research was insulin which, as well as being relatively small in size and available in large quantities, had strong clinical implications in the understanding of diseases such as diabetes. He developed a method of marking the end amino acid and splitting it off from the insulin. The end amino acid was then identified and the process repeated. By this painstaking method, Sanger showed that a molecule of insulin contains two peptide chains made of two or more amino acids that are linked together by two disulphide bonds. It took eight more years finally to identify the 51 amino acids that make up insulin.

The evolutionary mythology of randomness at the molecular level persisted for many years to come. Here is how the famous French evolutionist, Jacques Monod, described Sangar’s breakthrough work in the evolutionary classic Chance & Necessity:

The first description of a globular protein’s complete sequence was given by Sangar in 1952. It was both a revelation and a disappointment. This sequence, which one knew to define the structure, hence the elective properties of a functional protein (insulin), proved to be without any regularity, any special feature, any restrictive characteristic. Even so the hope remained that, with the gradual accumulation of other such findings, a few general laws of assembly as well as certain functional correlations would finally come to light. Today our information extends to hundreds of sequences corresponding to various proteins extracted from all sorts of organisms. From the work on these sequences, and after systematically comparing them with the help of modern means of analysis and computing, we are now in a position to deduce the general law: it is that of chance. To be more specific: these structures are “random” in the precise sense that, were we to know the exact order of 199 residues [i.e., amino acids] in a protein containing 200, it would be impossible to formulate any rule, theoretical or empirical, enabling us to predict the nature of the one residue not yet identified in the analysis.

To say that in a polypeptide the amino acid sequence is “random” may perhaps sound like a roundabout admission of ignorance. Quite to the contrary, the statement expresses the nature of the facts. [Vintage Books Edition, 1972, 96]

In fact the protein amino acid sequences are not random any more than an English sentence is random. But if you don’t know the language, it may appear random, such as this sequence of letters: “modnartonsierutan”. But appearances can be deceiving. Reverse the order and add a few spaces, and the sequence becomes: “nature is not random”.

Standard tests of randomness show that English text, and protein sequences, are not random. Nonetheless evolutionists continued to promote this view. A 1986 paper described globular proteins as having “random sequences” and that the physical requirements for such proteins are commonly inherent in random sequences.

Likewise as late as 1990 evolutionists claimed that the distribution of oily amino acids in protein sequences could not “be distinguished from that expected for a random distribution.” Thus proteins could have “originated from random sequences.”

All of this proved to be false and is yet another false prediction of the metaphysically-driven evolutionary thought.

Monday, November 18, 2013

The Mystery of Extreme Non-Coding Conservation

No Plausible Speculations

Evolution is unique in that while it is well known amongst evolutionists to be a fact, its predictions often turn out false. Consider this new paper from the Royal Society on “The mystery of extreme non-coding conservation” that has been found across many genomes. Years ago an evolution professor told me, in defending the claim that evolution is falsifiable, that if functionally unconstrained yet highly similar DNA sequences were found in different species, then evolution would be false. A few years later that is exactly what was discovered. In fact, the DNA sequences were extremely similar and even identical in different species, and when they were altogether removed from mice it made no detectable difference. Hundreds of tests showed no significant difference between mice with and without long stretches of these DNA sequences. Did the professor agree that evolution was false? Not at all. For the fact of evolution goes far deeper than scientific findings and failed predictions. Nonetheless, ten years later, the mystery of extreme DNA conservation remains.

As the paper explains, there is currently “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” This failure forces us to draw upon the typical explanatory mechanisms. The evolution of these extremely conserved sequences must have been abrupt and rapid, occurring in “short bursts.”

And since some of these sequences are found across a wide range of different species, the sequences, and whatever selective forces preserved them, must have been present very early in evolutionary history. On the other hand many of these sequences point to evolution’s nemesis, lineage-specific biology.

Some of these sequences are extremely conserved within lineages, but not across lineages. This forces us to conclude that the ancestral sequence first somehow arose in the common ancestor, later evolved independently in the different lineages which arose, became completely different in those different lineages, and then finally each of these different sequences, in the respective lineages, somehow became essentially unchangeable.

As is typical of the evolution genre, all of this is expressed in teleological terms. Here is a paragraph from the paper that is loaded with evolution’s Aristotelian tendencies:

Lowe et al. proposed that, within vertebrates, there have been three distinct periods of CNE [conserved non-coding element] recruitment around specific groups of genes. They suggest that this pattern is the result of regulatory innovations, which led to important phenotypic changes during vertebrate evolution. Prior to the divergence of mammals from reptiles and birds, it appears that CNEs were preferentially recruited near TFs and their developmental targets. This was followed by a gradual decline in recruitment near these genes, accompanied by [a recruitment] increase near proteins involved in extracellular signalling, and then [a recruitment] increase in placental mammals near genes responsible for post-translational modification and intracellular signalling. An analysis of CNE gain in the primate and rodent lineage has found that CNEs are either recruited near genes which have not previously been associated with CNEs, or are added near genes which are already flanked by CNEs. The interpretation was that the first set of genes is enriched in functions pertaining to nervous system development, whereas the latter contains genes involved in transcriptional regulation and anatomical development.

This example of teleological language also illustrates how the commitment to a theory can lead to a loss of parsimony. That is, in order to accommodate new and contradictory findings, additional explanations must be added to the theory. It becomes more complicated and less parsimonious. Here is how the paper summarizes these findings of extreme sequence conservation:

… despite 10 years of research, there has been virtually no progress towards answering the question of the origin of these patterns of extreme conservation. A number of hypotheses have been proposed, but most rely on modes of DNA : protein interactions that have never been observed and seem dubious at best. As a consequence, not only do we still lack a plausible mechanism for the conservation of CNEs—we lack even plausible speculations.

Reasonable speculation and even solutions to extreme sequence conservation may come in the future. But today’s science once again highlights the unique status of evolution.

Saturday, November 16, 2013

Another God of the Gaps Warning

The Ultimate Protection

Theory protectionism comes in many forms. One of the most common protections for the theory of evolution is the so-called God of the gaps warning which casts evolution criticism as an argument for the existence of God that is from ignorance and therefore a danger to one’s faith. This warning appeared again this week when Mark Shea used it against Intelligent Design in the National Catholic Register.

Shea is thought provoking but makes several mistakes that are typical (no, ID is not a theistic argument, it is not an appeal to inexplicability, and the history of God of the gap arguments is nothing like Shea’s portrayal). But nonetheless the God of the gaps warning is another powerful metaphysical mandate for evolution. The many scientific failures of evolution become irrelevant and even disallowed. It doesn’t matter how the science bears on the theory, it is always protected.

Tuesday, November 12, 2013

Origin of Life Solved (Again)

And Again, And Again, And …

Alexander Oparin’s 1924 prediction that origin of life research would be solved “very, very soon” may have been premature, but now, almost a century later, evolutionists have apparently found their much needed solution. In fact they have several solutions.

Evolutionists in Cambridge, England, for example, have discovered that life began with strands of RNA in a cold environment. “There's no reason why self-replication couldn't occur” that way, explained one evolutionist.

Meanwhile evolutionists in Italy found that life might have inevitably arisen from DNA and the protein synthesis machinery self-assembling in solute-rich, spontaneously-forming liposomes.

On the other hand, evolutionists at Cornell University have discovered that proteins can be made in a clay hydrogel. Fill the spongy material with DNA, amino acids, the right enzymes and a few bits of cellular machinery and you can make the proteins.

But evolutionists in Texas have discovered that life began in dark, hot, isolated environments of craters with hydrothermal vents that served as incubators for life. Convective currents brought organic molecules together, including RNA and proteins which emerged simultaneously. The discovery is apparently monumental. As one evolutionist exclaimed, “This is what we’ve all searched for – the Holy Grail of science.”

Oparin’s prediction may be late in coming, but now it seems that the cup runneth over. Not only has the problem been solved, but several times over with many different solutions.

That is, according to evolutionists.

In fact these various studies demonstrate nothing close to the origin of life. The claims—that these findings demonstrate how life could have arisen, how certain pathways are inevitable, and how they have found the Holy Grail of science—are contradictory, ridiculous and exaggerated. They have no basis in science.

At best they are simply stealing molecular machinery from cells or finding patterns which say nothing about the origin of life unless evolution is assumed to begin with. At worst they are silly, unrealistic just-so stories.

Religion drives science and it matters.

Sunday, November 10, 2013

Alfred Wallace: Evolution’s Creationist in the Closet

Coming Out

The fact of evolution does not refer to survival of the fittest, natural selection, gradualism, common descent, or any of the dozens of other subhypotheses but rather to evolution’s core idea that the species arose naturalistically. How it occurred is an open question—the theory of evolution. That it occurred is not in question—the fact of evolution. That makes evolution an all-or-nothing affair. If you don’t agree that science reveals the species arose strictly by natural causes and nothing else, then you’re not an evolutionist. In fact, according to evolutionists, you are a creationist. That is their term not just for those with a particular interpretation of Genesis. That is their term for anyone who doesn’t accept the fact of evolution. It doesn’t matter how many of evolution’s subhypotheses you accept.

That makes the case of one Alfred Russel Wallace rather interesting. With his centenary of passing observed this past week there has been a resurgence of interest and praise for evolution’s co-founder. There now is even a statue of Wallace at the Natural History Museum in London. Wallace is receiving his much deserved recognition, but all of this is a bit awkward because Wallace was, according to the evolutionist’s own terminology, a creationist.