I have written much about the vast improbabilities of whether DNA and proteins could have formed for the origin of life and changed in a functional way for the diversity we observe. There are other major scientific developments that relate to the Darwinian Theory of Evolution that go beyond these probabilities. I won’t go into a lot of detail, but will try to give a clear summary and have some references to read if you are interested. Then I want to mention a new group of scientists who have rejected the current Darwinian Theory of Evolution (also known with a few variations such as neo-Darwinism), and who have collectively put up a new website called The Third Way. I'll conclude by addressing the title of this blog post: Total-Natural Evolution.
Protein stability and Epistasis:
Proteins work through their physical makeup of their sub-parts, called amino acids. These have various shapes and charges, and with the help of other proteins, chains of amino acids often fold into a larger, specific shape for the over-all protein. The chains may fit together with other proteins to do the specific job. So the total protein machine may have thousands of amino acids.
Darwinian evolution theory depends on chance changes to genes that code for these amino acids, and therefore to chance changes of amino acids. At first, scientists did not know how many changes in amino acids would affect the ability for these proteins to fold and work as they should. Many believed the proteins could run through all kinds of differences in order to find new functions. But in the last few years, experiments have shown that it takes only a few of these changes to ruin the internal energy balance needed for the protein to fold properly. It might tolerate 2 or 3 changes, but after that, the internal stability usually plummets dramatically. It not only can't find new functions, it can't do its own work. I refer to a research paper by Tokuriki and Tawfik, "Stability effects of mutations and protein evolvability," Current Opinion in Structural Biology 19, 5 (Oct. 2009): 596-604.
In further work on this issue, researchers compared organisms. The scientists found that if they had changes of amino acids that experimentally ruined a protein, the changes could be found in various organisms, but were “compensated” by other specific amino acid changes that balanced the internal energy (and therefore stability) of the protein. However, this was not good evolutionary news after all. They believe these compensations kept the “bad” amino acid change from reverting back to the original, which turns out to have better function, and therefore evolution is limited.
These findings were for studies on one protein at a time, but other researchers have realized that there is a diminishing return on most cumulative protein changes. The term used is “epistasis” and often two or more newly changed proteins will not work together as well as the original ones, or a second change will not be as effective after the first change. These results have implications for protein function in various species, in that the changes do not allow transfer of function from one species to another. You can read an abstract of the research by Breen et al., "Epistasis as the primary factor in molecular evolution," Nature 490 (Oct. 14, 2012): 535-538. "Don't let the word "evolution" fool you because this is about lack of it.
Proteome discoveries:
“Extensive Cataloging of Human Proteins Uncovers 193 Never Known to Exist,” Johns Hopkins Medicine News Archive, May 28, 2014, reported that researchers have found almost 200 new human proteins. Because of the circumstances, the scientists expect many more new proteins to be found. That is because they were found in areas that were not normally considered “protein-coding” regions. A professor at Johns Hopkins, Akhilesh Pandey, stated, “the human proteome is so extensive and complex that researchers’ catalog of it will never be fully complete, but this work provides a solid foundation that others can reliably build upon.” Kind of boggles the imagination.
The research paper is Min-Sik Kim, et al., "A draft map of the human proteome," Nature 509 (May 28, 2014): 575-581. Though on the Internet you have to pay for the article, I’ve requested it through inter-library loan.
The Third Way:
The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.
I don’t know how the findings about Creationism are inconsistent with empirical evidence, since God is able to do all things. But that discussion is perhaps for another time. The point here is that they are claiming Charles Darwin’s Theory of Evolution is false. In scientific terms, it is falsified.
James Shapiro, the first scientist listed on The Third Way website under “People,” is a prominent microbiologist teaching at the University of Chicago. He has been telling folks that Darwin is dead for over a decade. Shapiro proposes the Third Way in a theory called “Natural Genetic Engineering.” The only problem is, he is still trying to make a case in another way for totally naturalistic causes.
Also claiming that Darwin's theory is wrong is Eugene Koonin, listed further down the People page. He is the Senior Investigator and the leader of the Evolutionary Genomics Group in the Computational Biology Branch of the National Center for Biotechnology Information (NCBI). This is the headquarters for comparative genomics, the field now possible through the whole gene sequencing of living organisms since 1995. As their data grows, they can see that these genes do not take the routes predicted by Darwinian evolution, and Koonin has clearly written about it. In the linked 2008 article he says the "Tree of Life" concept is undermined and a new conceptual framework needed. Yet he has been summarily ignored by the press and so-called science promoters and even “real” scientists.
If you read the papers and books listed on The Third Way website, you'll find these scientists loud and clearly tell the reasons why Darwinian Theory is not a fact. At The Third Way website under People, click on the individual scientists' names. You will see statements such as that from Denis Noble, another prominent biologist:
.... all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved. Moreover, they have been disproved in ways that raise the tantalizing prospect of a totally new synthesis...
Since it is becoming apparent that single amino acid changes are not possibly able to form the mechanisms for life, the underlying assumption for those like Shapiro is that segments of DNA that form domains are able to "mix and match" in order to form new proteins. There are elements in DNA that were experimentally found to be able to "jump" from one place to another. However, human DNA has 3.2 billion base pairs. How are the bases that form the proteins supposed to "know" where to fit in with the other DNA to make a new protein? There could have been only 10^50 organisms to play out the various combinations even in an old Earth. If DNA skips around substituting various groups of bases, it may still miss the ones that are functional. In a small example, if AAAGGGTTTCCC becomes AAACCCTTTCCC, you may instead need AAAATTTTCCCC for a specific new function. Though many proteins may use similar domains, there are many that are very different from each other. Douglas Axe reports that various species of just one small organism (E. coli) have been found to each have almost 1000 different domain structures (page 11 of the link). In the meantime, as described above, the new proteins can only tolerate a few changes to amino acids before they become completely worthless. You have all these molecules doing jobs and having to be arranged the right way so the right DNA can be copied at the right time. And yet we are supposed to believe that all these segments of DNA can be easily substituted so new proteins can form?
I nickname this type of biological theory "Total-Natural," which describes a totally materialistic basis for biological science in contrast to begin able to consider the Supernatural as a possible, or partial, cause. The concept of "total-natural evolution" is the worldview that totally naturalistic forces led to the origin and entire diversity of life. Total-natural is really the bottom line of the argument between materialists and Creationists. It's more to the point than the often-used "macro-" and "micro-" evolution arguments. Evolutionists say that macro-evolution is just the cumulative effect of micro-evolution. If there are at least some influences of the supernatural in the origin and diversity of life, our presence here is not explained in total-natural terms. There could be both supernatural and natural influences on diversity, but even differences in species are showing that many of the unique features are coded by orphan genes which are not related to others: Khalturin, et al., "More than just orphans: are taxonomically restricted genes important in evolution?" Trends in Genetics, 9 (Sept. 25, 2009): 404-413. And genes themselves are not the whole answer to development, as you will also find. Life has supernatural undertones.
If you have believed Charles Darwin’s Theory and are desperate to have the worldview of a total-natural origin and diversity of life, the best you have, as Denis Noble says, is a “tantalizing prospect.” I would ask you to reassess why you are so against the supernatural (or for theistic evolutionists, against direct supernatural Creation). It is wonderful to be able to believe in God and to increasingly appreciate His creative powers. Please don’t let anything, anyone, or any theory stop you from reaching the truth.
