Cookie Evolution

Often, people who misunderstand how the theory of evolution is supposed to work do not realize the vast complexity of biological mechanisms. They look, for example, at fish and land animals and imagine changes in environment are all it takes to bring about transformation from one species to another. All you have to do is invoke small steps.

To those who know more about biology, the formulation sounds a little like this:

“Cookie Evolution.”

• a. One of my cupboards has a baking goods storage environment and therefore wheat randomly became flour and cane syrup by chance transformed into sugar to fill this space.
• b. There was an empty and therefore potential environment in my cookie jar.
• c. By chance, my flour and sugar randomly combined with butter and eggs from my refrigerator environment.
• d. The combined features evolved when they passed through an oven environment.
• e. My cookie jar environment got filled by nature alone!

The same could be said for birthday party environments being filled by birthday cakes, etc., but you get the picture. These are called “just so” stories because they state in part what is there but do not explain anything in a truly scientific way. You can use your imagination to make up a scenario, but that does not mean it actually happened that way!

Researchers, university professors and other so-called science promoters say things and show their videos that look good to the public on the surface but are often theory instead of fact, or at most partial facts without showing what is missing.

Does it stop science to think that God supernaturally created some animals and plants directly? Looking at my “Cookie Evolution” above, it is much more logical to assume that thinking people were behind the making of flour, sugar, and butter, bringing the ingredients together in a beneficial proportion and cooking them optimally for the best outcome. New discoveries about wheat or sugar cane, for example, would never replace the need for the involvement of living agents. I believe there is a point at which we can say that new discoveries about science will not displace the need for a Creator.

Even if feedback mechanisms seem to help organisms adapt to the environment, the proteins and other physiological systems must be there to make it work. With every species, new proteins, called ORFans, are found, at the rate of about 1 in 10^70 being functional (see my previous post for further info HERE). This is what so many evolutionists skip over completely without any attempt at explanation.

What can a layperson do about false information? Try to look at the raw facts. The word "evolution" is inserted into a great deal of published scientific papers whether it is proven or not. Just skip over the word and see what was really discovered about genes, proteins, molecular mechanisms or whatever the focus of the experiment. 

And you also have to consider what is not proven. Give a fair hearing to Creationists because they are the ones who are willing to look at this side. Do not discount what they say just because they belong to a certain group. Look at credentials—there are more and more Intelligent Design advocates and Special Creationists coming from the most prestigious learning institutions of our day.

Most importantly, be honest with yourself. This can be painful, as I know from experience. But I also know that a change in perspective can be very, very liberating.

Catholics believe in the virgin birth of Jesus Christ. Right there we are looking at a supernatural genetic occurrence: the change of two X chromosomes to one X and one Y in one generation.

Personally, I think there may have been some cases in which one species may parent another that is not that far removed from it. On the other hand, I do not believe an ape of any kind gave birth to a human, either with intermediates or without. I think God created humans directly in a supernatural way. This is called Special Creationism (SC).

Jesus Christ knew human nature. He warned followers that we would be insulted for our faith in Him but He also said we would be rewarded for that very persecution (Matthew 5:11-12 NABRE). This is not to say we should promote SC for rewards alone. It is to say that if we believe in SC, we should have the courage to say so, to help others see what is true.

I find that the more I learn about biology, the more I think that what stops science is the unwillingness of many individuals to look at it straight in the face.

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.

Science in US Schools

There is a very interesting article at Answers in Genesis (AIG) about the history of teaching Creationism and evolution in US schools. The article is by Lael Weinberger, "Evolution in US Education and the Demise of its Public School System," Answers in Genesis (Jan 15, 2005). AIG is a group associated with the teaching of Special Creationism, the belief that God created humans and animals directly in a supernatural way. The article tells about certain judgments in the courts that have turned teaching in classrooms toward evolution and away from Creationism.

One important trial in 2005 was in Harrisburg PA over whether a textbook could have a disclaimer that introduced Intelligent Design Theory in the Dover School District. It ended in favor of the evolutionists. The Wikipedia description is HERE.

There had been a fight in Texas in 2013 over the science textbook to be used in the classroom, and the evolutionists won so that their textbook was chosen. That story is related by Casey Luskin, "What's Wrong with the Miller & Levine Biology Text Book?" Evolution News (Feb. 3, 2014).

The American Association for the Advancement of Science (AAAS) has played a prominent role in responding to efforts in Kansas, Pennsylvania and elsewhere to weaken or compromise (as they see it) the teaching of evolution in public school science classrooms. An article relates this activity by AAAS Staff, "Evolution on the Front Line," AAAS (June 30, 2013).

These are among the major happenings in our schools that have directed public science teaching toward evolution, although the fights continue in the states to introduce and/or follow bills for academic freedom. An example is given by Sarah Chaffee, "From Political Scientist Jeff Sadow..." Evolution News (June 23, 2016)

Though many people believe evolution is the answer to our existence, many have other beliefs. There should be a way for facts to be examined in the classroom in an equitable way.

Black Lives Matter

The Black Lives Matter (BLM) movement is very much in the news and on Internet chatter. The BLM group asserts that black people are treated differently by police than whites. I’d like to share on my blog a similar comment about BLM to what I made on the Catholic Answers Forums (CAF) website.

Some people are very unhappy with the BLM movement, equating it with bad behavior of blacks against police. Others sympathize with the blacks and believe their complaints that they are treated differently than whites by officers. Who is right? I don't believe we are getting to the bottom of racial divides.

Many people take for granted that the black race came from non-humans in Africa and then groups of individuals came North and evolved further into the white race. I have read a scientific paper from a major journal by Stergachis et al., "Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution," Science 342, 6164 (Dec. 13, 2013): 1367-1372. It is a technical title, but in the description of the experiment the text explains that a group of black people are assumed to be less evolved than whites in order to determine the mode of evolution of biological molecules.

The most significant of the researchers findings may be independent of this assumption and more information about the research is given by Stephanie Seiler,  "Scientists discover double meaning in the genetic code," UW News, Dec. 12, 2013. However, it seems there is no other way to say it but that some whites believe they are more evolved than blacks, and these whites include academic research scientists. Would that not cause some very bad feelings among the blacks? Would the Black Lives Matter’s group have some reason to believe they are treated in a different manner, such as in the history of Planned Parenthood eugenics? It could be that blacks and whites both are affected in their behaviors by this common mindset, perhaps subconsciously but in some cases blatantly.

However, if a person believes in direct supernatural creation of humans by God, s/he has no question of who is most evolved: no human is significantly different from any other human.

I treat these themes, among others, in my book, Biotech Swirl. I encourage you to read this FREE BOOK which you can reach at the link HERE or clicking on the picture of the book in the right column. Download it and/or read it online. Literature often helps us think about these issues and I hope this book may do so for you.

Nature's Abilities

In my last post I had a picture of Francis Bacon, the originator of our modern scientific method. Now I have another Francis, Dr. Collins, who led the Genome Project which made known the entire makeup of human genes. He is an esteemed scientist and deserves a great deal of credit for making the human genome available to all persons. In contrast, several companies were trying to discover the makeup at the same time and wanted to get commercial patents for it! (This is unimaginable and yet they wanted to own the human genome!)

Dr. Collins also did work on disease related to genes, and made significant contributions in this way. He is a Christian, and has written a book about his conversion called The Language of God. It is hard to go up against what he says, and yet no one is perfect. The Intelligent Design community is at odds with him because he believes that biological life and evolution occurred entirely without direct supervision from God. At the same time he thinks the universe, with its fine-tuning, is the result of God's handiwork. The term for people who believe in evolution with God in the background (to the point of not being allowed to touch it) is "Theistic Evolutionist."

One might ask, why quibble? Well, hopefully these differences are not enough to set Christian upon Christian. But there are a few problems. First, the people like Collins who believe God did not create biology supernaturally end up acting as if it is already proven He didn't. It is not.

Secondly, they teach children as if it is already proven He didn't. That is wrong both morally and in a scientific sense. Science is about evaluating what we know and interpreting it correctly. Morally, they convince children in a dishonest way what they want them to believe instead of telling them the truth.

Third, Theistic Evolutionists deride those who have other ideas. Instead of having both views as possibilities, they exclude the one they don't like. It is all right to have a hypothesis, such as neo-Darwinian materialistic evolution, but unless it is proven, you need to make room for other hypotheses. These people don't. They are disdainful of ID advocates because they fear that ID will destroy incentive to learn more. That is wrong and unfair. Research will continue as long as man has curiosity, which will be always.

It is only fair that ID people should allow for the materialistic view. It is not a matter in this case of what you think is scientifically correct. It is a matter of respect for other people's opinions and beliefs. If educators want to teach children materialistic evolution, they should teach ID right alongside it. Right now, the facts point to, if not already prove, Intelligent Design of biological life and evolution. (To see some of these facts, go through my ID and Creation posts under "Topics at Blog" in the right column.) For believers it would follow that, as it looks now, it is reasonable to think that God supernaturally intervened.

At one discussion about evolution that I attended, a man said he likes to enjoy the creativity of nature. I've seen that sentiment at the BioLogos Foundation website established by Francis Collins. They look at the cell's complexity and imagine nature to have made it. To me, that is like a man who goes away to work during the day, and his wife cleans, buys groceries, does laundry, takes care of the kids. Then she makes a meal that is on the table when the husband returns. He says, "Isn't nature wonderful, that it can put this meal on the table and take care of all the household needs?" Or even, "Honey, I know you somehow had a hand in this, but isn't nature impressive?"

Does God feel unappreciated? Perhaps no more than people whose work is ignored.