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 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:

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 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...

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 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.

Mission: Faithful

Though I said at first that I wouldn't put my book Mission: Faithful into a single digital file, I eventually did just that. You can click on the image to access the free PDF file of Mission: Faithful. If you want more details of its journey to my blog, read the rest of this post.

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 local 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.

(2019 Update: I decided to do as I did with Unto Others and get a few books printed. Now they are in a few local libraries and I have given some to friends and family.)

To me writing is not about money. I quote a part of Proverbs (from NIV). 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. 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. (2019 Update: I'm glad to say I finally was able to put this into a single file and it is now on my blog.)

When you talk about marketing, that is about as high-pressure as I get.

Biotech Swirl

I am happy to present my new fiction book, Biotech Swirl. Just click on the image for the free PDF file.

Biotech Swirl is a medical mystery thriller set in the current explosion of biotechnology.  The Catholic Chaplain Jan Pace is pulled into the dark side of scientific research when Dr. Hunter Balik suspects dangerous genetically engineered bacteria infecting several of his patients and asks her to help him investigate. Though she is not a medical expert, he feels she is trustworthy and he frankly needs a friend. As they proceed, they fear bio-terrorism but the crimes seem personal and murder can’t be discounted.

Dr. Balik, who practices at Fenwood Hospital in West Michigan, has a harsh bedside manner and has made no time for relationships. Though he resents the workaholic habits of his physician parents, he is repeating their mistakes. As Hunt and Jan work together, she attends to his spirituality as much as investigating the mystery.

Though the story starts with a medical crisis, the plot leads to persons with the tools and know-how to manipulate genes and with disturbing disregard for life. The suspects include a biotechnology business director who desires her company to embrace human embryonic stem cell research, a professor who wants to develop made-to-order genetically enhanced babies and an in-vitro fertilization clinic manager with questionable motives for disposal of the unborn.  The reader encounters today’s culturally misguided sense of “bioethics” through these and other characters.

Dr. Hunt Balik starts on this dangerous investigation without friends or faith. Jan Pace confronts potential terror. Somehow the two of them must summon the courage to overcome the deadly threat.

Please enjoy this new medical thriller for free! It is also in EPUB format, with that link in the page accessed on the right column. If you do not have readers for PDF or EPUB files, you can get free ones at app stores.

I hope Biotech Swirl will be engaging and thought-provoking for you.

God's Not Dead

My husband and I went to the movie, God’s Not Dead (Pure Flix Entertainment, 2014), last week. It was a surprising box office success and from the reviews I’ve read, many liked it. But a wide variety of people, from atheists to Young Earth Creationist Christians (YECCies), didn’t.  If you know the premise, you know why atheists don’t like it. The main character, Josh Wheaton, is a college student who is in a philosophy class where the professor wants to skip the section of his class in which he spends time convincing students that God does not exist. The professor insists the students write “God is Dead” on a piece of paper, sign it and hand it in.  Josh politely refuses, and so is assigned the task of standing before the class and defending his faith. Atheists either deny the movie is realistic or take the side of the professor who is clearly not the hero of the movie.

The reason some YECCies don’t like it is because Josh Wheaton argues for the existence of God by using the science of the Big Bang and Darwinian evolution theories. Both support an Old Earth, while YECCies believe in direct supernatural Creation of the planet and living species about 12,000 years ago. In addition, though the Big Bang broke through older theories of an eternal universe, both Big Bang and evolution theories now are supported by the scientific community under purely naturalistic explanations.

I learned from an interview by Dave Hartline, "God's Not Dead," National Review, March 29, 2014, that the screenwriters, Cary Solomon and Chuck Konzelman, are Catholics. I was surprised because the movie has an Evangelical feel to it.  I have to give these writers credit for “getting it” about the Catholic New Evangelization movement that is supposed to be in effect.  This actually means EVANGELIZING, folks!!!

This leads me to say there are things I liked about the movie and things I didn’t. I have to give a mild spoiler alert: skip down a few paragraphs to the images if you don’t want to know any more about the movie before seeing it. First for the likes: the student takes God seriously. He actually thinks about what his actions have to do with his faith. He stands up for what he believes. I agree with the movie premise that the pressures are against believers in academia, and if you don’t believe this, just follow the Intelligent Design blog, Evolution News. They keep a running tab on the discrimination against anyone who thinks biology is designed, especially in academia. Let’s not forget that Intelligent Design Theory, much less Creationism, is not allowed in public schools.

Another thing I liked about the movie is that the tone for the most part was not hostility toward unbelievers but hopefulness for them to realize the truth. I felt this attitude came across several times especially in side-plots, and became more apparent at the end. This is a difficult attitude to take but necessary for all Christians.

For the part I didn’t like, it has to do with one of the points made by Josh when “defending” God’s existence. Like many other Creationists, I believe direct supernatural formation to be the best explanation for biological complexity. I don’t go along with the main character’s explanation of God directing evolution through seemingly random events. Though this is the line taken by many Catholics, I feel that if we had a clearer picture of biology, this is the very place where we can make an effective argument against the extreme scientism of today. Scientism is the cultural belief that science will answer everything and God doesn’t exist. Today’s cultural climate is where the movie premise is hitting the truth. The effect of science on philosophy is large, and well-known evolutionists take the lead in the discrimination and downright prejudice against believers.  It starts in academia and has filtered throughout the whole culture. Unfortunately, lawmakers and judges who hear arguments for teaching exclusively evolution in public school often are swayed by this cultural attitude.

The deep problem is that the people held as experts inform the public that evolution is true.  What can the public believe? They, like Josh Wheaton, must learn for themselves.  This training is just what I’ve been saying we need for the youth of today to defend their faith.  There are problems with that right now in the Catholic culture too, some of which I have discussed in other posts. But putting that aside for now, let me (again) show you biological complexity.

Photosynthesis is present in Cyanobacteria (pronounced sigh-ann-oh-bacteria). These organisms are among the very first the evolutionists tell us were on earth ("Origin of Life," Berkeley Evolution 101). They take energy, in this case light from the sun, and convert it to the building blocks of life. These are necessary for proteins, DNA, and other components. Evolutionists might tell you there were simpler systems earlier, but because they exist now, it means somewhere along the line the present systems had to form. Plus, the entire photosynthesis system would have been evolutionarily early because these very early fossils show the pigments and bi-products of photosynthesis. And that means the atoms which form them must have been lined up in the precise way of functional proteins and not just a jumble of any old atoms. 

The images here show the overall photosynthesis pathway and three of the protein systems close up. The components are mostly proteins, although there are a few other types of molecules. I will shortly talk about proteins in terms of their sub-units called amino acids, but I have made rough estimates of the total number of atoms in the system. This is a very rough estimate, so if anyone has the exact number, I’d be glad to hear it.

The set of proteins and other molecules known as “Photosystem I” are seen in the second image (NCBI Structure entry 2O01). There are over 50,000 atoms in this large set of molecules. That means they have to be specifically lined up by the cell enough to be in working order. Describing the system, the Abstract at the link says:

This structural information extends the understanding of the most efficient nano-photochemical machine in nature.

Photosystem II, pictured in the third image, has over 83,000 atoms in specific order (Wikipedia entry HERE).

When we add the atoms of photosynthesis molecules (very approximately), the cytochrome molecule has about 1500 atoms, and another integral part, ATP Synthase, has about 90,000. There are several other proteins to help with electron transfer, so we are looking at a total of around 225,000 atoms in a specific order for the photosynthesis system. Also necessary is a functional membrane so that an electro-chemical gradient can build to work the ATP synthase machine, and of course the genes which act as the template to make the proteins, the other proteins needed to copy the genes and make the proteins, and the regulators. The products of the photosynthesis complex go on to an entirely different set of molecules so they can be used to make the basic component of the parts of the cell (sugars, DNA, proteins, fats, etc.). 

When figuring probabilities that all of these parts could come together by chance, we often use the sub-unit of the protein called “amino acid.” This is because we can then assume the cell is already in working order and we can eliminate the chemistry involved in bringing all the atoms together. All biological amino acids have at least 10 atoms. The Photosystem I complex alone contains about 3100 amino acids.  Because there are 20 types of amino acids in proteins, this would bring a possibility of 20 to the power of 3100 combinations. Converting to a more familiar base 10, that would be 10 to the power of 4030 (written 10^4030). Even if the Earth is 4 billion years old, it could not have had more than 10^50 organisms (based on volume of water). In bacteria, a mutation only happens once about every 300 generations. The DNA that mutates during replication for another generation represents each "search" or "try" for the combination of amino acids that will function in the necessary way. The discrepancy is overwhelming for even one of the sets of molecules, since all reactions in a 14 billion year old universe are less than 10^150. And the total Photosynthesis machinery consists of about 15,000 amino acids (counted from composite parts in the RSCB PDB).

Yet, when confronted with these facts, the evolutionist will say something like, “Maybe there was exchange of genes so that part of a previously functional protein became part of this system.” There are several answers to this. First, if evolution were true, all proteins would have to arrive at their functional state by chance. Even a short protein, about 70 amino acids long, would need 10^90 tries to get the right combination of amino acids, and that assumes that the genetic machinery is in full working order and there is an intact membrane. The number 10^90 represents the estimated total number of atoms in the visible universe. Some proteins do need the exact lineup of amino acids, such as histones. And for those less exact, the proportion of functional proteins is still only one in 10^65 or so. Second, even if there are two or more changes at once, the organism will then miss out on the other “tries.” In other words, if the DNA base code changes from CCCCCC to CCCCGG from one generation or organism to the next, it will have missed CCCCCG, which might have been the necessary combination for function (the actual number of bases would be larger but this gives the idea: you get 2 G's instead of 1 G). When you are dealing with random, the genes don’t “know” which parts are functional and which aren’t.

These are the types of facts every Catholic should know.  It is not that difficult, and this is the argument that should be set forth. We should not weakly accept naturalistic, materialistic evolution theory. The student in the movie, Josh, said in so many words that though evolution seems random, God could be directing it. This is the argument I hear from Catholics and other Christians and it is not a valid argument. The problem is not with the paradox which is posed. The problem is that though they say evolution, they imply that biology SEEMS RANDOM when biology actually DOES NOT SEEM RANDOM. The photosynthesis machinery needs to have proteins which are folded in exact shapes and have the exact matches to fit with critical molecules in order for our cells to work. It sure does not seem random to me. The atoms are arranged in specific order so they can make products like no other in nature.

There may have been a time when biologists were overcome by the number of species of beetles and in that way biology may have seemed random to them.  Then we discovered that DNA does mutate in a seemingly random manner. Perhaps the changes within DNA that come about when an organism reproduces may eventually be proven to have some explanation, so that small part of cell biology may actually SEEM random to us now and not be. But that small part of biological metabolism has not been proven to provide the specific order that is necessary for fully functional biological systems. Therefore we can’t say meaningful evolution seems random when we refer to the formation of all working systems that are present in the full diversity of living organisms, including those systems that make living beings diverse.

The arrangement of these atoms is more complex than simple random connections. Although chemistry depends on probabilities of atom movements, it also depends on attractions of types of atoms and the concentrations of each. Since scientists don’t know the exact original conditions on Earth, they cannot tell us that materialistic origin of life is a fact. Likewise, they cannot exactly account for the photosynthesis mechanisms in life. Evolution is not a fact because no one is able to lay out the scientific details of how such systems formed.

These are the types of arguments we need against the evolutionists who feed the public with “proofs” of evolution. There may be small changes after many generations of bacteria, such as in R. Lenski’s experiments with thousands of generations of E. coli at Michigan State.  However, there are explanations for these that do not point toward totally materialistic, naturalistic evolution (discussion at CreationWiki HERE). As Michael Behe points out in the link I've just given, most changes are losses of function that somehow help the organism survive but decrease its overall efficiency. Rarely, a very small change in protein can lead to better function, but it is a tiny part of a much larger biological system which already works.

The need in our culture, as demonstrated in the movie God's Not Dead, is for Christians to learn the truth and then to evangelize. Let us do so!

Free Reads!

I have added pages to my blog that hold FREE reading material.  One is a booklet, Heaven’s Passport, and another a book, Unto Others. You can click the images here to get to the books. The pages with further descriptions are accessed by clicking the images in the right column of the blog.

I had written Heaven’s Passport back in 2005. It addresses some common questions about Christianity in a straightforward way. It is meant to be a tool for evangelization, and can be read online or downloaded. It can also be printed into a 20-page booklet by anyone with 5 regular-sized pieces of printing paper and therefore passed along to others in this form.  I had it on my blog for a while but had taken it off.  I had done the cover of Heaven’s Passport myself and it was not very professional-looking.  So I decided to make the effort to purchase a cover designed by a local printing business, and it looks much better. Heaven’s Passport can be read in one sitting or in sections, and I hope you will take the time to read it or download it now for perusal and sharing. It is in PDF form, and most devices already have readers for these files. If you download and need a reader program, you can get a free one at an app store.

Catholics are called to a “New Evangelization,” and there are a variety of ways we are trying.  In some ways the Internet provides unlimited horizons, but on the other hand there is a lot of resistance to the message. It is important for each individual to realize that he or she is someone whom God cares about and wants as His own. And so I am happy to ask anyone who comes here to feel very special. We Christians want to tell YOU about the salvation that is possible through Jesus Christ.

Another page holds Unto Others, a fictional mystery with Catholic themes. It is also FREE. I put it in two file forms (EPUB and PDF) so you can choose what is best for you.  Again, free reader programs are available in app stores if you need any.

I hope you will take the time to check out these pages.  Heaven's Passport and Unto Others are meant to be thought-provoking and enjoyable too. Catholics need to widen their horizons in the world of literature, and I’m trying to do my part. Read my books and see what you think!

Some Research

A full text research paper is available online by Guo, Choe and Loeb, “Protein Tolerance to Random Amino Acid Change.”  PNAS  101, 25 (June 22, 2004): 9205-9210.  PNAS, the publisher, stands for Proceedings of the National Academy of Sciences of the USA. The researchers wanted to know the probability that a protein would lose its function with one random amino acid replacement at any (also random) position on the protein. Amino acids are the sub-units that make up proteins. The researchers reported on their own experiments and also compared their results to others of a similar nature.

Their own experiment was carried out on a human protein nicknamed AAG.  Its chemical name and biological activity are described in the paper. They found that the probability it would lose its function with only one amino acid replacement was around 34%, and the reviews of other experiments at the time showed similar outcomes. One of several interesting aspects of the paper concerned “indel” mutations.  Indels are where several DNA bases are inserted or deleted instead of a single base change in a gene which is copied to make the protein.  They translate into extra or deleted amino acids. These indels were not even considered in the numbers for calculation because, although they were present in low percentages, “they invariably produce protein inactivation” (p. 9206 on the PDF version). Later the authors modify the description to non-3bp (base pair) indels, but still give a value of “≈1” (almost equal to one) to represent almost 100% indel destruction of proteins.

Guo's experiment was on a single protein, and other research may show that not all indels lead to total destruction of proteins.  However, it is very likely that a lot of destruction from indels would be taking place in an organism before any indel would bring about innovations to form a new functional protein. Guo et al. also quoted other experiments in which researchers replaced amino acids until 100% of the particular protein was inactivated.  The figures ranged from 5-16% of replacements to do the job.   

One of the citations used in the research paper above was for work done by Douglas Axe.  Axe earned his PhD at Caltech and went on to post-graduate work at Cambridge. He is now director of the Biologic Institute in Washington State where he does experiments on proteins and protein systems. The Institute publishes the BIO-Complexity Journal (link for Archives HERE). He has had articles published in the Journal of Molecular Biology and other peer-reviewed scientific journals, contrary to the widespread claim that Intelligent Design advocates have never accomplished this feat.

A paper well worth reading is Douglas Axe, “The Case Against a Darwinian Origin of Protein Folds,” BIO-Complexity (2010). You can read the abstract at the link above and the site has a link to the PDF article. There are pictures of proteins and their sub-units (such as the image to the left) and Axe explains why the makeup of proteins is specialized.  These are not conglomerations of simple repeating units that fall together in a warm pool. The sub-units, called amino acids, are structured intricately and when put together in various ways have biologically important and specific functions. Although Axe uses large words and numbers, he also tries to explain what he says in simpler terms.

The challenge for evolutionary theory concerning the origin and development of proteins is what Douglas Axe describes as “The Sampling Problem.” Many people do not recognize the vast combinations even small collections of molecules can make.  As Axe says, “Amino Acid chains a mere 12 residues long [composed of 20 possible kinds of amino acids] …can be built in 4 quadrillion ways (20^12=4x10^15).” A relatively short protein of 69 amino acids has about 10^90 combinations. 10^90 is the estimated number of particles in the known universe.  These numbers are not to be brushed off.  It takes reproduction of generations of organisms to try out ("sample") new amino acid combinations, and that takes time. Billions of years are not even close to being enough.

Histones Stand Alone

The bacteria are single-celled organisms that live just about everywhere. E. coli is fairly well known because it survives in human intestinal tracts, it has been extensively studied, and it can cause food poisoning.  It has many different strains and the K12 is a common research type.  Rounding off, the K12 sub-strain MG1655 has about 4.5 million DNA base pairs (a base is one of 4 types of molecules used for the DNA code) and about 4500 genes. The sizes of bacterial cells also vary, but one organism is about 1-2 microns.  A micron is 1000th of a millimeter (which is 1000th of a meter). There are 25,000 microns in an inch. An average E. coli bacterium is therefore about 1-2 25,000th of an inch. And yet each organism has millions of DNA bases that need to be organized and compacted so the code can be copied at the right times to produce proteins, the working molecules of the cell, and other products. The proteins make energy from light sources, manufacture the cell wall, participate in reproduction, and all the other processes needed for life. Yet another job is the bending and organization of DNA.

The long DNA molecule in many bacteria is “circular.” The DNA is one loop instead of separate chromosomes as humans have.  The cells don’t have a separate chamber for the DNA as ours do.  But a lot still has to happen for the molecules to get their jobs done.  One of the ways the DNA is organized is by what is called “supercoiling.” The above picture is from Willenbrock and Ussery, "Chromatin architecture and gene expression in Escherichia coli," Genome Biology 5, 12 (Dec. 1, 2004). The full article link gives more of an explanation, including in the abstract:

Two recent genome-scale analyses underscore the importance of DNA topology [geometric properties] and chromatin structure in regulating transcription [DNA copying] in Escherichia coli.

Chromatin is shown near the middle.

The authors of the above article elaborate on the shape of the DNA, which is much more complex than pictured. They say, “DNA has sequence-dependent structures, just like proteins, and certain sequences tend to coil in three-dimensional space.” I had written in January about new research that had revealed another language in DNA beside the one which codes for proteins (the link is HERE). Though that was new research and no doubt will undergo further testing, there is no denial that DNA has the ability to communicate with the molecules that regulate its output.  But DNA has even more talents, since it has to fold and organize beyond simple mechanical compression with the help of proteins.

Besides having its variety of shapes, another way DNA is regulated is by the proteins which bend and condense it. They can move from one part to another so that a particular gene is either copied or not depending on the needs of the cell. There are several proteins which bend and regulate DNA in bacteria, one of which is HU. The second image shows two HU proteins (one silver, one gold) bending two loops of DNA (blue and purple), from NCBI entry 1P51. There can be as many as 15,000 HU proteins in one bacterial cell. These particular structures pictured each have 94 amino acids, their own subunits which have to be in correct order for the protein itself to fold and then bend the DNA.

Bacteria are known as “prokaryotes” (pronounced pro-carry-oats).  As well as not having an inner wall around the DNA (nucleus) like the cells in animals, they have other differences as well.  There is another prokaryotic domain of life known as “Archaea” (are-KEY-ah). The grouping of biological life is shifting since it became possible for scientists to learn the entire codes in the genomes of species.  The fact is that the sequences are not falling in place.  But the “Tree of Life” project Root Page (link HERE) explains:

The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly [common ancestry] of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon.

They used to think that Archaea evolved to Eubacteria (true bacteria) which evolved to Eukaryotes (true cells with an intact nucleus and other organelles as found in humans). But they found very different stories. Using as an example the proteins which bend and organize the DNA, there are none even close in bacteria to humans.  The histone they’ve found to have a similar-looking fold to humans is in Archaea (Bacterial Chromatin, Dame and Dorman, editors, [Springer, 2010]).  But this is a structural similarity, not sequential (Sandman and Reeve, "Archaeal histones and the origin of the histone fold," Current Opinion in Microbiology, 9, 5 [Oct. 2006]).  The sequences are as far from Eukaryotes as any of the others (less than 15%).  These are short proteins, so the matches or lack of them are obvious (see image below).

It is true that not all species have been sequenced.  But these DNA-bending proteins are so greatly different that it is obvious that they could not all have come from the same source.  Even if another animal species showed up that had histone sequences half-way similar to those of a human, they could not account for the spread of differences already found. And so far, none have shown up with Archaeal-like histones (species Methanothermus fervidus), as you can see in the boxes in the image below. (This result is from a BLINK database which compares proteins from different species, run in February 2014. The query page is HERE and the Uniprot number was entered into Blink: in this case P48781). (Update 9-16-2018: When you click the given Blink link you are now re-directed to another comparative genetic database called BLAST. The Blink database was discontinued in May 2017. For more information you can read about Blink HERE.)

The "similar" Archaeal histone protein that is mentioned above is 69 amino acids long (M. fervidus). Since there are 20 biological amino acids, the possibilities for this length of chain are 20^69 (20 to the power of 69, using ^ for an exponent), or about 10^90 (a 1 with 90 zeroes after it). Contrary to simulated computer programs of mutation, there is nothing to stop the DNA from mutating the bases which cause the protein to work correctly.  Natural selection would eliminate those organisms which mutated from useful to less functional (they die or reproduce less). So even if the proteins have a small proportion of the same amino acids when compared now, say 10%, there would still have to be an average of about 10^90 tries to get from one of the structures to the other. (I want to add that as of Feb. 2014, the human histone H3 [Uniprot number P68431] entered in BLINK for matches, brings up 0 Bacteria, 0 Archaea and 0 Viruses.)

Using the volume of an E. coli and the volume of the Earth’s water to calculate the quantity limit of possible life on Earth, there could have been no more than 10^50 of these (or therefore any-sized) organisms on Earth in 4 billion years (Nelson, see reference at bottom). The bacteria only mutate less than one base per generation and not all DNA mutations cause protein changes. So even if the 10^50 number included a change in an amino acid each time, there would very, very probably not be enough of the bacteria to find the right combination to transform from one functional DNA bending protein to one of the others that we have found experimentally. In the meantime they would have had to sort through all kinds of useless proteins because after a certain number of mutations the proteins lose their ability to do their specific job. The RSCB Protein Data Bank describes histones this way: "The histone proteins are perfectly designed for their jobs...Even slight modifications can be lethal."

The last picture is a group of histones in humans (center) which wrap DNA (outer strands) in order to organize its long double helix into chromatin and chromosomes (NCBI entry 1KX5).

These comparisons are just for histones.  Even if human histones are compared to other proteins to find a supposed source, many of the thousands of proteins in animals and plants are much longer than histones and/or have no obvious ancestors. They would have to undergo much greater evolutionary transformations. Many scientists and the media do not bring these types of things to attention.  They seem to want you to think evolution is easy.  I guess it is wishful thinking on their part, but why do they wish these things are by chance?  Life is better when you increasingly appreciate the Creator of all.

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Nelson, Fred.  "Needed: A New Vocabulary for Understanding Evolution." Perspectives on Science and Christian Faith 58, 1 (Mar. 2006): 31. The link HERE goes to a PDF file of the article.

Images 2 and 5 are from NCBI:

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. "MMDB: 3D structures and macromolecular interactions." Nucleic Acids Res. 2012 Jan; 40(Database issue):D461-4