Important Research

Many people seem swayed to believe in totally materialistic evolution for various reasons. But if you are going to be "scientific," you have to be willing to look at all the evidence. What many are missing are the huge differences in the species that greatly overwhelm the similarities.

It has been 30 years since a very significant scientific article about proteins was published by researchers. One of the scientists is Robert T. Sauer, Salvador E. Luria Professor of Biology at MIT. He has a BA from Amherst in biophysics and a PhD from Harvard. The paper and the findings are technical, but I will attempt to explain, so I hope you will try to read through. The paper is by JF Reidhaar-Olson and RT Sauer, "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor," Proteins, 7, 4 (1990): 306-16. From here I will refer to the article as RO&S, and the abstract can be found in the paper title link at the NCBI PubMed website. NCBI stands for National Center for Biotechnology Information.

The Lambda phage is a virus that infects bacteria, in this case E. coli., and it has a protein called repressor. I have included an image of repressor (purple) next to a DNA strand, from Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). More information on this protein is at RCSB PDB entry 3BDN.  Citation for RCSB PDB: Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne, "The Protein Data Bank," Nucleic Acids Research 28, 1 (Jan. 1, 2000): 235–242.

Proteins are made within the cell, the basic unit of biology, of every living organism. DNA codes for proteins, which do much of the work of the specific cells. The alpha helical regions to which the RO&S paper refer are among the particular parts of proteins that give them their function. The lambda repressor was the protein they were researching, although they used just part of the protein for the experiments. The substitutions in the title refer to the subunits of proteins, called amino acids. There are 20 kinds of these in most proteins and each is made of a certain set of atoms. The researchers wanted to see how many amino acids could be interchanged with the parts of the protein still remaining functional. They used an experimental method to make random substitutions in these subunits within the repressor protein. The amino acids are numbered and they used two sets: 8-23 and 75-83 (Using 1-92 amino acids of a 237 amino acid protein).

I will use the term "permutation" here, meaning the evaluation of proteins must include specific order of amino acids and their repetition, unlike "combination" which does not require a specific order. (I am saying here, though will elaborate in another post, protein probabilities are not evaluated like card games.) RO&S reveals that though there are a large number of subunit permutations which can make working protein folds similar to the particular one they studied, the proportion of functional ones of possible permutations are only about 1 in 10^63. 10^63 is the number 1 with 63 0's following it. (I like to use a caret ^ when writing what are called exponents because it is easier but (for example in this case) the number can be written 10⁶³ . The first or lower number is the base and the second or upper one is the exponent. The exponent tells you how many times to multiply the base times itself to get to the final number it describes.)  1 in 10^63 is a very, very small proportion of permutations that work. Relating to evolution, the less proportion of functional choices there are, the less the probability you will get one to form by chance. There has to be something to choose from (coming from mutations) in order to get any selection!

The authors of the RO&S paper claim the gist of this research was supposed to show the admittedly large number of possibilities for the amino acid subunit combinations to make protein folds (the term “degeneracy” they speak about in abstract). However, the paper showed something way more significant, the proportion of non-functional to functional as already described. To give the researchers credit, they do talk about the limitations of content of proteins in the abstract, but not the specific findings. A reader has to follow the paper to the second last paragraph of the article to find it, and the paper is behind a paywall!

If you are at all interested in reading the whole RO&S article, the abstract page from my link has a link you can follow to get access to the paper. But it is through Readcube and there is a charge and as far as I know you can't get it free online. If anyone knows it is available online, please let me know. However, I got my copy of the entire paper through inter-library loan for free a few years ago. Inter-library loan is still available, although I don’t know if it always provides the whole paper. Or, you may live close to a University which allows access to their journals. I was able to read several other articles in this way. Fortunately, there are some research articles which are available online in complete form, and I have an important one here with a link (Fredric P. Nelson) which I discuss below.

Another significant fact about the RO&S research was that, although they used different methods than some theoretical work done earlier by Hubert Yockey who applied Information Theory, their work closely backed his. Yockey's research was done in the 1970s and gave indications then that proteins are very rare. I have a previous post about this work. He used a protein involved in respiration, Cytochrome C, and compared it in different species. An image of it is included here from Uniprot entry P99999. Citation for Uniprot is Uniprot Consortium, "UniProt: a worldwide hub of protein knowledge," Nucleic Acids Research 47, D1 (Jan. 8, 2019): D506-D515.

A link is here to the abstract of the paper by Hubert P. Yockey, "A calculation of the probability of spontaneous biogenesis by information theory," Journal of Theoretical Biology 67, 3 (August 7, 1977): 377-398. He included a few more chemical factors and estimated a chance in the range of 1 in 10^65 for nature to select a Cytochrome C sequence randomly.

Then other experiments were done and numbers proved to be again similar. An important scientist has researched at University of Cambridge. The Abstract in one of his papers is from Douglas Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology 341, 5 (Aug 27, 2004): 1295-1315. It shows a 1 in 10^64 proportion for a low-function domain and 1 in 10^77 for overall short protein function. Perhaps a general number of 1 in 10^70 could be used for simple proteins, but many are much more complex and therefore would be even more rare. The numbers compare to 10^65 atoms in our galaxy to 1^90 particles in the universe.

The Darwinian claim is to take the fact that DNA randomly mutates (or changes) as time goes by and conclude that the resulting proteins, which are a little different from previous ones, will lead to new species. The fittest, or best, of these changes in particular individuals allows them to survive and leads to fitter organisms.  Evolutionists say the 4 billion years of the Earth's habitable environment allowed for enough changes for humans to emerge. But organisms change only a little at a time. Bacteria do not even have one change per generation.

There may be some small, natural neo-Darwinian evolution in life, but there are other considerations. We must include large differences between some proteins as well as small ones. Some resemble each other and are functional and may have come from random mutations of DNA down the generations. Maybe even a protein that is slightly broken from a mutation may stop an antibiotic from binding to a bacteria's wall thereby making it resistant to the antibiotic. But there are many critically necessary proteins that are not even close to others in terms of their subunit arrangements and could never have evolved one from another, in a Darwinian sense, even in four billion years.

Fredric P. Nelson calculated the maximum number of organisms that could have existed on the Earth by water volume in 4 billion years at about 10^50. You would not have enough organisms in 4 billion years to try for proteins that are only available at the rate of 1 in 10^70. Fortunately, this whole paper is available online. Page 31 and the footnotes are especially interesting since his calculations are there. The link is here for Fredric P. Nelson, “Needed: A New Vocabulary for Understanding Evolution,”  Perspectives on Science and Christian Faith 58, 1 (March 2006): 28-36.

We need to look at a few more discoveries. As scientists discover the DNA (and thereby protein) codes of more and more species, they are finding a certain percentage of each, around 10% to 30%, are not related to any other species. These as a group are known, among other names, as orphan, or ORFan genes (a gene being defined as a protein-coding part of the DNA chain). Among the many scientific papers that have been reporting this finding is by Arendsee, Li, and Wurtele, "Coming of age: orphan genes in plants," Trends in Plant Science 19, 11 (Nov. 2014): 698-708. This finding is related to the limit of numbers of organisms that have been available to mutate for "tries" for functional proteins just mentioned.

Concerning life's origin, a minimal, natural free-living organism (not a lab creature which is given nutrients) has been estimated to need around 1000 proteins to survive by NCBI researchers Koonin and Wolf, "Geneomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 2008): 6688-6719. Even if some were closely related, the independent probability of only 10%, or 100, functional proteins is about 1 in 10^7,000. 

Pertaining to both origin and evolution, N. Tokuriki and D. Tawfik researched protein stability in terms of thermodynamics and kinetics. They found only a few substitutions could be tolerated before the proteins became severely impeded in their function. Though there can be compensation, this severely limits any ease of evolution. The article is N. Tokuriki and D. Tawfik, "Stability effects of mutations and protein evolvability," Current Opinion in Structural Biology 19, 5 (Oct. 2009): 596-604.

So no, these numbers are not wiped away by the Darwinian duo of random mutation and selection of the fittest. We must keep in mind that for evolution,  the first step, random mutation, must happen first inside the organisms in their reproductive cells in order to form any new proteins that could be selected. This vast improbability of functional proteins overwhelms even the number of organisms that existed on Earth. No mutation rate could bring about new proteins on a viable level.

Also, I don't believe quantum physics either explains or explains away proteins. QP is real and admittedly very strange, but chemistry is also real and is described by its own physical rules. If that were not true, we'd all be constantly slipping in and out of reality (granted, some think this is exactly what happens).

The rarity of functional protein folds is one of the features that convinced a well-known Yale computer expert and professor to recently exclaim Darwin’s theory proven false. His essay is David Gelernter, "Giving up Darwin," Claremont Review of Books, XIX, 2 (Spring 2019): 104-109.

There are admittedly many, many things to learn about proteins and DNA. That is important for creationists to keep in mind. However, for scientists to insist on totally naturalistic evolution by random chance, they deny what is true once again. In Darwin's day, they said the cells were blobs which had little to no internal activity. Then scientists denied DNA and proteins were rare due to specificity, which is proving to be wrong. They claimed DNA was filled with junk which is now being revealed as useful. All their false concepts delay scientific progress, yet they claim the creationists are the ones who are detrimental to it. Thankfully there are individuals who do not stop investigating when the consensus resists change. 

One book about Catholics and evolution is by Fr. Michael Chaberek, OP, Aquinas and Evolution (Chartwell Press, 2007). Chaberek asserts that at the end of the nineteenth century, "Thomists universally rejected the Darwinian theory of origins" (p. 10). He lays out his thesis that Aquinas was not an evolutionist and today's science would not change his mind. In the Forward to the book, Logan Gage, PhD, Chair of the Philosophy Dept. at Franciscan University of Steubenville, writes, "Culturally it has been easy to dismiss worries about Darwinian evolution as a 'fundamentalists' Protestant problem. Additionally, we Catholics have a 'Galileo Complex.'"

Some Christians insist that God would only create life in a certain materialistic way. I remind everyone that God does as He sees fit, and many Christians look at the living wonders of the world and think God made at least some of them in original species through Special Creation. New scientific discoveries are actually supporting our view.

For us, science is the study of created physical things. We need to show the world it is not only reasonable to be a believer, it adds the vital meaning to our lives. Let us praise the Lord, through Jesus Christ, for His Creation.

Book Files

It's been on my mind for a long time to check whether the very limited selection of file types for the books on my blog (PDF and/or EPUB) are adequate. I have put this off in tandem with setting the whole blog aside. Well today, in a brief but enlightening period of time,  I  found that Kindle, iPhones and iPads can display PDF files. I also know that android can handle PDF since I can view it on my nook. Android also uses EPUB (as when I get books from the library onto my nook). I really would rather not get into further Kindle conversions unless there were any requests, which so far has never happened.  So, I made the rather obvious choice to go with what I already have!

My main concern was that the books' PDF files did not show up well on my laptop when I opened them. My guess is that to best view them you will have to download the file and read it from your own computer. The browsers have versions of their own PDF readers, and the well-known Adobe Acrobat Reader has free software for reading PDF files. You can get more information on the Adobe software HERE.

I apologize that this is probably at least partly a low-tech cop-out.  But if anyone requests something else, I can try to accommodate, perhaps even with their help. I am just glad to feel I am doing something with the blog again.

The coming of September with school starting has made me want to get in a regular routine of reading and writing. I feel like I am getting my goals done each day when I read several verses of a study Bible with notes and a few pages of some other books. Now I'm even writing a blog post! I am hoping I can stick even loosely to my schedule.

Thanks to anyone who visits.  Feel free to drop me a line.  💌

Three Month List

I'd like to present a list of excuses for why I haven't written here for 3 months, but no use whining. Everyone is busy, yet some people can keep their blogs going without gaps. Still, even though I have slacked, l believe it's a good practice to add a post once in a while in case I ever get back to this blog on a regular basis. If anyone checks they will see I haven't forgotten it altogether. I actually can't believe Google has been kind and consistent enough to keep the blog site going in the way it has. I'm sure they get something out of it but to give them credit, it is a benefit for those who use it.

Technically, I have done some things on the blog that aren't reflected in the posts. I added my book, Mission: Faithful which I edited last year (see the picture on right to access). And now I hope to go through the files of my other books to update them.

Also, I will go through my posts from the beginning, which was back in 2008. I am sure there are a lot of links that are outdated, and I wasn't always careful about my style for citations. I hope to make improvements in that area.

I do find purpose in thinking about the blog and in writing. So thanks for stopping by and someday I may get back to posts which have more than 3 month's worth of dates between them!
😉

Trying My Best

I am going to use personal stresses as the reason for delays in previous promises I made to look into the programs that carry my blog's e-books. I want you to have the optimum reading experience and am not sure which possible downloads are the best for which devices. But I just haven't had the time to look into it. Among the stresses in no particular order: both my laptops, one old and one new, have had repeated technical problems; my mother who lives 350 miles from me has cancer and needs regular treatments; now I have my own health problems and don't know where that is going. I find it hard to get back into the blog with these things going on.

I know there are not many who come to this website and perhaps none of these promises to update or at least check for better download possibilities are necessary. I guess I will have to discern depending on future events. In the meantime hope that anyone reading will check out the books and posts, as I have invited before. And leave a comment or two if you so desire.

Tomorrow is Easter. I hope you have a very blessed one. 🙏

The Perspective of Worshiping God

There has been discussion about whether the Biblical God of Abraham is the same as the Christian God. I know many think He is the same, but I think there is some confusion and the argument depends on perspective. I would like to present my thoughts. I think what I will say is also applicable to the argument that “we all have the same God.”

First we have to keep straight whether by the term “God” we are referring to the ultimately true (Catholic) God or to the concept of God within each human.

Catholics believe the Trinitarian God is and always has been God of all. Our Catholic God is the Father, Son and Holy Spirit, three Persons and one Essence (CCC 253). But the other perspective of “god” would be from a human person's point of view: what that person considers as his or her spiritual creator and/or controller of him/herself and surroundings and therefore worships. We know of examples of ancient Romans, Greeks or Native Americans who believed in multiple gods, some of which supposedly created then others who controlled fertility, rain, etc. Yet we Christians believe our Trinitarian God was ultimately their God because He was the one who really created and sustained their lives even though they didn’t know or worship Him as He is. We don't consider their concept of God to be correct and therefore from our perspective they worshipped false gods. Catholics believe humans are affected by fallen nature and deception is part of that. Perhaps some of these groups had inklings of the true God but others carried on with the false ones. They may have even had interactions with demons through this false worship.

Ancient Jewish people worshiped one God, and some still do, in the sense of one Person, the Father. When Moses asked His name, God answered “I am who I am” (Exodus 3:14), and said this would be his name forever (and He is 3 in one forever). They believed “The Lord our God is One God” (Deuteronomy 6:4). I believe that from the current Christian perspective, the God that interacted with Abraham and Moses and the Old Testament Israelites before Christ came to Earth was the true God, our God. I believe because of the revelation of the Bible which is the inspired book of my faith and because the Father had an especially close relationship with the Israelites since Christ was born from that people. On the other hand, our true God allowed the Israelites at that time to think of Him as one Person, which was not fully complete. He acts with His own purpose and the time had not come to fully reveal Himself. In the belief of the people, He was a different God than ours, even though there were references to the Spirit and the Messiah in the Old Testament. Even though they pictured Him differently from what He really is, I don't think He would have considered them worshiping a false God since it is what He told them and probably knew they would not understand the concept of 3 in one at that time. Later, however, God speaks of a New Covenant with His people, which is repeated by Christ in His last supper: “This cup is the new covenant in my blood, which will be shed for you” (Luke 22:20).

I believe since Christ came, whoever hears of Him is to worship the true God as a Trinitarian God and in no other way. Though we will never understand God fully, we believe He has revealed His nature and made it plain He wants all of us to believe in Jesus Christ as a Person of the Trinitarian God, our Savior from our sins. We still suffer from the fallen nature. From the Christian perspective, to worship God as only one Person is wrong. The human who holds that belief rejects two equally important Divine Persons who have one Essence. And therefore after a human person hears about Christ, to worship the Father alone is, from the perspective of the person who is worshiping him in that way, worshiping a different God than Christians are. To Christians, Jesus Christ is a Person of God. To non-Christians, He is not God.

This is why I also say that we can’t just let it go at “we all have the same God.” Though the true God is ultimately the same, what matters to each of our souls is that we declare Who our God is.

I think battles occur in the spiritual realm and correct human belief and worship of God are very fundamental to these battles. These days, human belief seems unimportant to many people. But I hold that what ultimately matters to each human being is Who or what we believe and in turn how we worship and speak.