Friday, June 6, 2014

Total-Natural Evolution

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: 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. The link for the paper is here and the reference is: Tokuriki N, Tawfik DS. Stability effects of mutations and protein evolvability, Curr Opin Struct Biol (2009), doi:10.1016/ .

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 are results found in the long-term evolution studies of the Richard Lenski Lab at Michigan State.

Proteome discoveries:

A news release from Johns Hopkins University titled, “Extensive Cataloging of Human Proteins Uncovers 193 Never Known to Exist,” 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 abstract, reported in the journal Nature on May 29, is here. Though on the Internet you have to pay for the article, I’ve requested it through inter-library loan.

The Third Way:

There is now a website, The Third Way, in which a group of scientists is openly claiming that the currently held Darwinian Theory of Evolution is no longer to be considered true. Here are the introductory words:
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 saying things like this 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. 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...
Unfortunately, these biologists still do not see the forest for the trees. They look at the reams of biological knowledge and still want to pack it all in physical laws. From what we know of physical laws at this time, there is no positive proof these laws can act as sources of biological complexity.

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. 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. 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.

Sunday, June 1, 2014

Mission: Faithful

Back in the day, as they say, I wrote my first book, Mission: Faithful. I self-published it, since it is not the kind of book many publishers, even religious ones, were interested in. Though the book is an action-adventure fiction, the underlying themes are about unity of Christian denominations and discernment among Christian individuals. Unity has not seemed to be a priority of denominational publishing houses. Perhaps that will change now that Pope Francis is actively encouraging it.

At the time, Barnes and Noble was open to promoting local authors, and I am thankful to have had a book signing at our nearby store. It was attended by friends and relatives, most of whom had already received the book free from me. To say I am not a dynamic marketer is a vast understatement, and I sold very few. So, I gave several to local libraries and a few to others and more or less called it quits.

At the time I published the book, printing businesses had not yet gone to digital publishing. They were using the old way of making a typeset proof or whatever they called it, and printing from there. The initial setup costs were high but the printing lower, so the more books you got, the less they cost each. However, I knew I would probably not sell many, and did it more for the promotion of the ideas than to make money. I did not want to order a large number. Unfortunately, my husband was of the “less cost per book” mindset, so we ordered one thousand of them.

I don’t know exactly how many I had left after my efforts at distribution, but it was a lot. I made room in the basement for all the boxes and they have been there for a long time. Somehow, this experience did not dampen my desire to write, and I self-published a fictional mystery, Unto Others, in 2008. Fortunately, by that time our printing businesses had acquired digital, print-on-demand capabilities and I ordered 100 paperback copies of Unto Others. I loosely followed the same pattern as the first book in my marketing, but this time did not have so many left over. This book also can be found at local libraries. I was not making money on it, but when I occasionally checked the status in the various library catalogs, I was pleased to find it was often checked out. At least people were reading it.

In the time since then, the digital age has truly come upon us, and people are reading books right from the electronic files. I’ve decided to self-publish my most recent book, Biotech Swirl, in the ePUB format, and plan for now to keep it at that. Boy, does that reduce costs! However, since it isn’t in a library, my quandary was whether anyone would ever hear about this book. It’s on my blog, but this is not a high-volume traffic kind of place.

So, I decided to take the extras of my first paperback, Mission: Faithful, and wrap one at a time in a plastic bag with a half-sheet filler that gives my blog address and pictures of the other book covers. I decided to place them in the community one at a time so that people can discover the free book inside the bag, read it and also be aware of my blog.
However, just after I started to place a few per week in various locations, I learned about the rich person who is anonymously placing envelopes of money in San Francisco and tweeting clues of their locations. It seems to have created a fad across the country where various groups and individuals are copying the idea (article about it here). This threw me off because I wondered if the people who found my book would have heard about the money envelopes and be disappointed at the lack of cash.

So I added a text box to the filler in which I quote a part of Proverbs (from BibleGateway). It talks about wisdom being more valuable than silver, gold and rubies. I remember reading that when I was young and it somehow stuck. As I get older, I increasingly appreciate and believe the words. In case you can't read it in the entire filler above, I have a separate image of it here.

Though we might have varying opinions on specific aspects of wisdom, I hope my books are wise, especially in the sense that I try to bring out, through the characters, ways our relationship with God affects our lives. The books are meant, like many fictional stories, to provoke thought about deeper things.

I wrote Mission: Faithful on a computer program so old that I would have to re-type it to make it available digitally. I am not planning to spend the time on that, but I have put Unto Others into accessible digital form. I also have a few non-fiction booklets available on the blog. The names are lined up as links under the top picture of the blog. You can read and download any or all of them, which I heartily encourage.

To clarify, I am not sending electronic clues like the millionaire to find my book. I don't tweet at all--I figure one Internet interface is enough for me. I just put each book in its individual bag at a variety of places where people eventually go by and hope it catches their attention. And when you talk about marketing, that is about as high-pressure as I get.