Saturday, September 29, 2012

Evolution (Not) Crucial in Antibiotics Breakthrough: How Science is Actually Done

Where is the best place to find low-cost, easy-to-produce, natural, robust and non toxic antibiotics? Easy, in our own bodies. Nature so often provides the solutions we are looking for and, as an aside, that is why the preservation of species from extinction is so important. In this case the solution is natural antibiotics which University of California at Berkeley researchers have confirmed to exist in the tails of certain proteins called cytokeratins. These proteins help our eyes, for example, ward off infections. The eye’s cornea is remarkably free of pathogens and the research reveals something about how these wonderful proteins work. Once again, however, the research was not motivated by evolutionary theory.

Proteins consist of a long chain of amino acids, attached one after the other. This chain, or backbone, is usually tightly coiled into a helix shape or stretched out into a strand shape. Occasionally the backbone folds back on itself and so adopts a turn shape. Proteins that are inserted into the cell membrane are usually helices for the helix shape can have a more oily surface to match the oily interior of the membrane.

The Berkeley researchers found that the cytokeratin tails apparently insert into the membrane of pathogen cells. The cytokeratin tails they investigated were 13 to 26 amino acids long and are rich in the simplest amino acid, glycine. Here, from the paper, are the sequences and their properties:

Glycine’s side chain is nothing but a mere hydrogen atom and as such it is the most flexible amino acid. So not surprisingly the cytokeratin tails do not adopt a fixed helix or strand shape, but rather a looser, less common, coil shape. It appears that the insertion of the tail into the pathogen’s membrane not only serves to immobilize the foreign cell, it also creates a pore in the membrane. Such pores are harmful to cells because they serve to neutralize the all-important chemical and electrical properties of the cell.

This new research is important for what it tells us about antibiotics and for what it tells us about science. Rationalists maintain that scientists must operate from a theory of origins in order to do science and that, in particular, that theory must be evolution. But science itself demonstrates that there is no such requirement.

Thursday, September 27, 2012

Beyond the Power of Accident

Just over a century ago a gracefully aging scholar quietly left the world with these wise words:

A young bird makes us laugh. When its feathers have grown, the same bird makes Shelley write an immortal ode. Such is the wonder of feathers. And how do they grow? Evolution can explain a great deal; but the origin of a feather, and its growth, this is beyond our comprehension, certainly beyond the power of accident to achieve. … The scales on the wings of a moth, have no explanation in Evolution. They belong to Beauty, and Beauty is a spiritual mystery. Even Huxley was puzzled by the beauty of his environment. What is the origin of Beauty? Evolution cannot explain.

Was this man a fundamentalist resisting the inexorable progress of science? No, this was evolution’s co-founder Alfred Wallace who believed evolution to be a good, but limited, hypothesis. Once again wisdom is justified by all her children for now, a century later, Wallace’s simple yet profound observations have been fulfilled. There is no scientific explanation for the origin of feathers, wings of moths, or untold other biological designs. Evolution is a fact, but not because it explains the origin of species.

Sunday, September 23, 2012

Here’s That New Paper Showing the Genetic Regulation Hiearchy

Ever since Mendelian genetics was incorporated into Darwinism, evolutionists have believed that the gene is king. Genes, they thought, determine an organism’s design or, in technical jargon, the genotype specifies the phenotype. This fit their view that the species originated from the natural selection of biological change which did not arise initially as a consequence of need but rather as a consequence of random, spontaneous events. Those random, spontaneous, events were, for example, mutations in the genes. And later when the genetic code, which translates the information in those genes into proteins, was found to be essentially universal throughout biology, the story seemed complete. For if the species were designed why would their genetic codes be identical? But today, so many problems with this story have emerged it is difficult to keep track. And new research continues to add yet more problems.

Aside from the non scientific claims underlying evolution’s metaphysics (what scientific experiment informed evolutionists that independently created species would necessarily have different genetic codes?), the empirical science has contradicted evolution’s story at every turn. Genes are not king, mutations show no sign of creating biology’s marvels in spite of evolutionist’s many attempts to coax them to show off their power, the genetic code has special properties and shows no sign of having been a “frozen accident,” and all kinds of new codes have been discovered that are not universal but instead are lineage-specific.

One interesting part of this on-going contradiction of evolutionary theory is the role of proteins referred to as transcription factors which help to regulate the expression of genes. The elaborate genetic regulation processes are fascinating and you can read more herehere, here, here, here, here, here, here, here, here, here, here, here, here, here, here and here. It highlights yet another chicken-or-the-egg conundrum, for proteins are produced from the information in genes, and yet proteins are required in that very production process.

One of the types of proteins involved are the  transcription factors which help to turn genes on or off. They bind to nearby DNA regions that flank the genes to influence the genetic copying machine. The DNA sequences in those flanking regions as well as the transcription factors are important in determining the genetic regulation.

But the action of these transcription factors is not universal or consistent across species but rather are lineage-specific. Evolutionists were surprised when transcription factor binding was found to be not conserved between mice and men, between various other vertebrates, and even between different species of yeast.  If a universal code confirms evolution then a non universal code contradicts evolution.

But there are more ways in which transcription factors and their associated DNA regions contradict evolution. For instance, those DNA regions have special properties that evolution must have somehow accidentally created. In fact, as one evolutionist explained, evolution must have created these DNA regions “which may allow evolutionary adaptation to novel conditions.”

In other words, evolution created special DNA regions so that evolution could then occur.

Another such complication is that transcription factors can not only start and stop the RNA polymerase copy machine, they can also pause the machine after it has begun. And other transcription factors turn off the pause, so the transcription process may continue. So astonishingly, evolution must have created these profound complexities from random mutations so they could then be selected.

Now new research adds to this story with a massive study of the interactions between transcription factors and DNA. The study found that the action of transcription factors falls into three distinct, hierarchical, categories. There are interactions that specify the basic cell type (muscle, skin, nerve, and so forth). Then there are interactions that specify the cell’s sub-identity (the particular type of muscle cell, for example). And finally there are interactions that specify the cell’s response to the current environmental challenges.

Of course evolutionists have no explanation, beyond vague speculation, of how such a hierarchy of mechanisms could have arisen spontaneously. But for now no such explanation is needed. Evolution is known to be a fact and so we can be confident that future research will explain all these apparent contradictions. That’s how evolutionary theory works.

Saturday, September 22, 2012

You Are What You Your Mother Eats

New research continues to reveal biology’s complex adaptation capabilities broadly referred to as epigenetics. Simply put, individuals not only respond physiologically to environmental challenges by modifying their DNA, they also pass such adaptations on to their progeny. It is, by any other name, the inheritance of acquired characteristics, a concept evolutionists have resisted for almost a century. Now researchers studying mice have found that a mother’s diet not only during pregnancy, but before pregnancy, causes intelligent adaptations to occur that are passed on to the offspring—a finding that once was cause for blackballing. Now, molecular machines that (i) sense environmental shifts, (ii) produce the desired response, and (iii) pass that response on to offspring arose by chance, and were later selected. What was once unacceptable anathema is now becoming orthodoxy in what we know to be the fact of evolution. As Darwin explained:

Whether the naturalist believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace and myself, or in any other such view, signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable; for he who admits this as a great truth has a wide field opened to him for further inquiry.

It isn’t that we know how life has arisen so much as we know how life has not arisen. That’s how science works sometimes.

Friday, September 21, 2012

Here’s an Example of Evolution’s Unavoidable Anti Realism

Though evolutionists think of themselves as realists—ruthlessly objective investigators interested only in truth—their naturalistic constraint ultimately leaves them with only anti realism. This is because any a priori restriction of the answer might exclude the true answer. If I decide my math homework must contain only odd numbered answers, then I’ll be wrong on those problems whose correct answer is an even number. I can round up, approximate, truncate, contort or whatever to obtain an odd number, but I will be wrong. For such problems, the only way to be right is to remove the a priori restriction. But evolutionists cannot do this. Foundational to their thinking is that the world must have arisen by itself, strictly via natural laws and processes. What most evolutionists do not grasp is that their extreme rationalism leads at best to anti realism, and at worst to skepticism.

Evolutionary theory has produced so many false predictions—and as a consequence has become so complex—that it is difficult to keep track. Evolutionists have approximated, truncated, contorted or whatever to obtain their mandated answer. The fact that evolution is a fact is underwritten by the rationalistic a priori constraint rather than the scientific results. The former has precedence because the latter is always a work in progress. Scientific results can change, so given enough time and contorting we may yet find that the science supports the rationalism.

In the meantime this commitment to method can lead to awkward moments, such as when the student asks how evolution created life and all its species, how it created such complexity, how it created such variation where it shouldn’t be, or how it created such similarity where it shouldn’t be, and so forth.

While brow-beating, intimidation, delegitimization, dismissal, mockery and funding threats are usually sufficient to check any such challenges, some evolutionists find safety in the ultimate defense: evolution’s latent anti realism. Scientific problems don’t matter because evolution need not track reality in the first place. It is simply a brute fact.

Descartes introduced the specter of anti realism to evolutionary thought in the seventeenth century when he advocated for naturalism regardless of truth. For when the true cause is unknown, “it suffices to imagine a cause which could produce the effect in question, even if it could have been produced by other causes and we do not know which is the true cause.” For Descartes, a theory could be fictional, but still useful.

Today, evolutionists dismiss scientific failure as inconsequential. Evolution need not produce true explanations, just useful explanations. The evolutionary tree has failed, for example, but as Joel Velasco explains, though evolutionary processes may not be tree-like, nonetheless the evolutionary tree model helps us to understand the world better:

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are tree-like. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models which contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called “the importance of tree-thinking.” …

We have seen that phylogenetic trees are ubiquitous in biology. The justification for the use of trees has traditionally been that evolutionary processes are in fact tree-like. This justification is faulty. Attempting to interpret phylogenetic trees in a literal way leads to the view that these trees entail many falsities about evolutionary history. Attacks on the universal tree of life thus appear to be justified. The goal of this paper is to argue that these attacks are not in conflict with the continued and justified use of trees and tree-thinking in biology. The use of phylogenetic trees can often be completely justified even if they are not entirely accurate representations of the world. Instead, these trees are models which contain idealizations. These models are used to better understand the world. Sometimes, for some purposes, a tree model is inappropriate. But often, trees are entirely appropriate and perhaps even the best models we have.

Modeling and idealizations are widespread throughout the sciences. There is no particular reason to think that systematics should be any different. Evolutionary history is complicated. It is a sign of the advancement of the science of systematics that we not only take advantage of standard modeling practices from other disciplines, but that we understand that this is what it is that we are doing. It is true that belief in the existence of the tree of life as the big, universal, grand unifying, scale-free representation of all of the history of life should probably go away (if indeed biologists ever did believe there was such a tree). Whether we can still talk about the tree of life as some modified version of this idea is, I think, an open question. Whether the problems with the universal tree extend to smaller trees as well will depend on the particular details of the case in question. But whatever the outcome of these debates, phylogenetic trees and the importance of tree-thinking are here to stay. The future of tree-thinking is bright as long as we can recognize the importance of tree-thinking without the tree.

Evolution’s predictions have consistently failed and the species do not form an evolutionary tree. These are yet more manifestations of evolution’s underlying anti realism. But evolution remains a fact.

Thursday, September 20, 2012

Crab and Locust Bones Optimized For Their Respective Functions

New research on the bone designs of crabs and locusts—whose skeletons are on the outside—has found that their high-tech composite bone material known as cuticle is formed into optimal geometries for their respective uses. The crab bone which the researchers analyzed undergoes both bending and compression and the bone’s design was found to be “an ideal compromise to resist these two types of loading.” The locust bone that was analyzed, on the other hand, mostly undergoes bending and was found to be “optimized for this loading mode.” Endoskeleton bones, on other hand, were not found to be optimized for these structural functions.

Monday, September 3, 2012

Self-Refuting Belief Systems

Relativism states that there are no absolute truths, but if true then that statement is an absolute truth. Likewise the statement that evolution is a fact, if true, means that we cannot know evolution to be a fact. Why? Because with evolution our minds are nothing more than molecules in motion—an accidental biochemistry experiment which has yielded a set of chemicals in a certain configuration. This leads to what Darwin called “the horrid doubt”:

But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind.

Today evolutionists agree that while a random collection of chemicals doesn’t know anything, nonetheless over long time periods and under the action of natural selection, phenomena which we refer to as knowledge, will and consciousness will spontaneously emerge. And how do we know this? Because evolution occurred and we know that it occurred. Therefore evolution must have created the phenomena of knowledge. The proof is left to the student.