2022 Creation Biology for Beginners

I have updated my Creation Biology for Beginners booklet. The booklet is for persons interested in the relationship between biology and religion. The discussions of science and religion in general have brought on a spectrum of opinions, from denial that one is affected by the other at all, to insistence that they are completely intertwined. I invite you to take a look at this FREE, short (16-page) booklet by clicking the link on the image or RIGHT HERE. I hope it will intrigue you enough to continue your educational experience with my 40-page booklet, Creation Biology, found at the link RIGHT HERE.

Thanks for your visit!  

New Creation Biology Cover

It's been an amazingly busy summer and my last blog post was over 2 months ago. But I've been working, with help, on a new cover for my Creation Biology, 2021 Edition, and am happy with the results. I offer this 35-page booklet free over the Internet but also will print out some paper editions as I seek God's guidance on its distribution. I know many people are writing about creation now, related to the fields of biology, geology and cosmology. This is my small contribution, gleaned from my formal education and continued reading. 

UPDATE 2-21-22: After printing out some of the booklets, I found the font too small to comfortably read. I thought I might as well check through it again and made yet a few more edits for clarity. So now it is the 40-page Creation Biology, 2022 Edition. You can click on the image for the direct link or get it RIGHT HERE.

I think there are very good reasons to believe that God made life and some species, or types, directly by supernatural means, called Special Creation. My booklet describes some details of biology and relates how improbable it would be for the present systems to be in place by chance. I try to be as clear as I can, and it is important for people to know these facts so they can approach the questions of Creation and evolution with as much information as possible.

Though people say that scientists will always discover more, at some point we accept certain scientific facts such as the existence of atoms and molecules. We may come to learn more about them, but enough has been clarified to believe they exist. The biological discoveries of the last few decades have been enough to clarify that random mutation of DNA and subsequent "selection of the fittest" is not a reasonable answer for the makeup and variation of life we see today.

Now that I'm done with this booklet, I'm trying to read more of the Summa Theologica by St. Thomas Aquinas, the great theologian.  He refers to Aristotle's Metaphysics quite often, which I had never read, so I am tackling that too. Those books will keep me occupied for a long time.

I hope that you will let my Creation Biology, 2022 Edition booklet occupy some of your time.

Creation Biology, 2021 Edition

I have been wanting to update my Creation Biology booklet and finally managed to do it in a 2021 edition. Like all my books and booklets, it is absolutely free!

UPDATE 2-21-22: After printing out some of the booklets, I found the font too small to comfortably read. I thought I might as well check through it again and made yet a few more edits for clarity. So now it is the 40-page Creation Biology, 2022 Edition. To access, you can click on the image or the direct link RIGHT HERE.

The purpose of Creation Biology has always been to discuss the possibility of direct supernatural creation by God of biological life. Though I have some of the same information in this booklet as previous ones, I feel this one adds even more to explain recent biological research and the implications. One new section describes some of the most recent discoveries in the Human Genome Project, and my "Evolution Conclusion" shows how a biological system which is given as a "simple" source for complexity by evolutionists, the Type III Secretion System, is itself complex. So click the link HERE or on the side column picture, and get to the page that takes you to the PDF file. As with the other books and booklets, you can download it if you want. There is a link for a PDF reader on the booklet page. 

Be sure to tell anyone you know that is interested in the controversy about Darwinian evolution that this is a thought-provoking booklet about the possibility, and even probability, that God created life directly by supernatural means.

PS -- I use the Word 2016 program for word processing. I can convert to PDF, but it has limits. The bad news is that you can't click directly to the endnotes on the last pages (34-35),  At least the PDF scrolls easily (once the file is all there), so to go to an endnote, remember what page you are on, scroll to see the note and then go back up to your page when ready. The good news is that the endnote hyperlinks work, so you can go to the references directly from the booklet. If anyone knows of an online converter that works with footnotes and endnotes, please drop a line.

PPS -- I do my own booklet graphics, so they are not perfect, but the links will take you to the original works. I will, however, be turning to a professional company for the cover for the new version. I'll post the change as soon as it's done!

Creation Biologists

The term "Creationism" is often associated with a belief in a young Earth of several thousand years. However, all Christian Creationism indicates a belief that God created our universe, life and diverse species. Therefore, some Creationists think a Big Bang, billions of years ago, started things rolling. The question many are grappling with is how, in the sense of in how much time and by what means, God did it.

Some Christians don't think it is very important for us to know the details. They say that faith in the Trinity (Father, Son, Jesus Christ, and Holy Spirit) is the focal point, and they are right about that. However, in the culture of our day, two of the factors that draw many people away from our faith are philosophical materialism and scientism, which go hand in hand. Scientists in general insist we may not even consider that God formed anything physical, such as a species (much less life), directly. Science, they say, has all the answers and religious belief only gets in the way. Many Christians therefore emphasize the need to be precise about where they think God truly came into the Creation process.

Humans are complicated and honest motives vary, much less accusations of dishonest motives from various sources. Christians are suspected of disguising the truth no matter our knowledge of facts, or being so unintelligent that we fail to see that scientists will figure it all out in the end. To make things worse, among Christians there are some deep disagreements of opinions, especially when it comes to evolution of life.

In contrast to Christians who believe God directly created life and at least some of its types supernaturally, there are advocates of "Theistic Evolution" (TE) who think God made species, including humans, through the Darwinian processes of mutation and natural selection. Their science is basically the same as the secular scientists' version, except that we are supposed to imagine God was somehow involved.

One of the main proponents of TE has been Francis Collins, MD, PhD, director of the National Institutes of Health in Bethesda, MD. He has made it a mission to convert Christians to Theistic Evolution. Why would this difference matter so much?

Dr. Collins promotes research that includes the use and destruction of human embryos and human fetal tissue. He encourages human cloning and human-animal chimeras, that is, the mixing of animal and human genetic material in single individuals. David Prentice, PhD, and vice president and research director of Charlotte Lozier Institute, a life-promoting agency, called for a replacement of Collins as director for NIH in an article in USA Today (April 25, 2017), linked HERE. Prentice provided background material that clearly documented Collin's stance on these issues. The link is HERE. Information on Dr. Prentice is HERE.

Collins says research on human fetal and embryonic tissue is needed for the sake of improving medicine. But this falls into the category of those in power profiting from the helpless and oppressed. Anyone who considers the human fetus and embryo “real” humans can see the problem.

Many people are convinced that the worldview of totally materialistic evolution blunts the idea of the dignity of humans and their worth. Though some think this reasoning does not follow, those who don’t see the value of the forming yet unborn humans may have subtly obtained this mindset from the very pervasiveness of the Darwinian theory, which is based on random events. How seriously should we take ourselves if we came about by accident? Even Christians become confused, especially with the emphasis our culture has, not only on science, but on philosophical materialism.

Another aspect of evolution in the devaluing of human life is the potential for racism. I have an article from a prominent research journal that describes a study about DNA. Though the “Out of Africa” human evolution and migration theory pervades our thinking, I was still shocked to see that the DNA of people of African descent was actually used as research material for “less evolved.” There have now been fossils of humans found in other areas of the world that have put this long and hard-held theory into question (see article HERE), and the whole theory of humans from non-humans should be put to rest this instant.

Many people fear Creationism stops science. But in just one example, Darwinian evolutionists had insisted that much of our DNA was “junk,” and this is turning out to be untrue. This belief had stopped science for many years, as well as other similar cases. An atom is an atom, no matter your faith. We can all make progress together.

“Creation Biology” (CB) is a catch phrase, since it doesn’t spell out all aspects of Creationism, including age of the Earth. But CB points out the falsification of Darwinian evolution no matter whether the Earth is 4-some billion years old or several thousand. CB infers that no human being was born of any other species. “Creation Biologists” can advocate that life itself was created supernaturally by God and that not all of the other diverse life forms came from a single origin. We can believe all human life is very special, created directly by God in His own image.

Creation Biology is obviously a subject of great interest to me. I would like to someday get involved in discussions at Catholic Answers Forums about Creationism now that I finished the latest CB series on the blog, with the related posts since October of 2019 in particular. Though I’ve been writing about biology a long time, I learned a lot in doing these recent entries and I am glad for the time and opportunity I had to do them. I’d like to share them more than I am doing by writing my blog alone, and yet I want to learn about some other subjects before getting tied up at the Forums, which looks pretty inevitable if you get involved with anything related to the subject of Creationism or evolution. I ask God to guide me, so I do my best to try to follow Him and trust He will use this work as He will. Thanks to anyone who has taken time to read my posts.

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.

Pseudogenes

Evolutionists have used what are called “pseudogenes” as proof of evolution. The pseudogenes are supposed to be broken genes that appear in multiple species that are alleged to have evolved from their ancestors. Many resemble functional genes as if there were random reproduction of the working genes and then decline of the original or duplicate due to generations of mutation and non-use. If the extra genes are broken, goes the thinking, why would they exist in various species unless they were passed along the evolutionary tree?

Fortunately, there are scientists out there who are actually studying biology. The pseudogenes are turning out to have very important functions, often concerning gene regulation. One report is by Cheetham, Faulkner, and Dinger, “Overcoming challenges and dogmas to understand the functions of pseudogenes,” Nature Reviews Genetics 21 (Dec. 17, 2019):191–201. Their article Abstract says volumes:

Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution.

There is increasing realization that there are reasons that some genes resemble each other. Ironically, these particular authors are still thinking in the evolutionary mode. Don’t they realize the “pejorative inference of the ‘pseudogene’ label” of which they speak comes 100% from evolutionists? But what at the end they say is true. Their reassessments may give them the ultimate insight: that evolution is very minimal in explaining the diversity and wonder of life.

A major study called ENCODE,  reported by the ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome,"  Nature 489 (Sept. 5, 2012): 57-74, showed that much more of the DNA in our cells is being actively used than researchers ever expected. One of these scientists is Dr. Francis Collins, director of the National Institutes of Health in Bethesda, Maryland. Before, they had called most of the DNA “junk” which they assumed was from evolutionary mutations. Dr. Collins admitted he was wrong in using the term “junk” and said he would no longer refer to DNA in that way.

Now pseudogenes, which the prominent evolutionists have used as one of their prime examples as worthless, is turning out as valuable genetic material that is currently undergoing much biomedical research which may lead to cures in cancer and other diseases.

Yes, genes mutate. I’m a doctor of veterinary medicine, I know about that. But I also know that the numbers of mutation and the precision of genetics don’t add up. 

When are people going to get over themselves and start thinking outside the box? When can we end the “Galileo Complex,” as Logan Gage, PhD, Chair of the Philosophy Dept. at Franciscan University of Steubenville, calls the extreme reluctance of Catholics to allow that the Lord may have touched His own Creation along the way?

Those who call Creationists "science deniers" often do not know the science themselves. They rely on the evolutionist leaders who, as we are discovering, hold back progress more than advance it.

It is obvious that humans are intelligent creatures who want to discover the workings of the universe, both for curiosity’s sake and to protect ourselves from harm. But we are not to be rigid, either. It takes more intelligence to reach beyond black and white, not less. It is way beyond time to do so.

Orphans, HGT and Secretion Systems

I'm going to give a line of reasoning that changes subject a few times, so I hope you will take your time and stay with me. I think part of the reason evolutionists get away with pushing their materialistic view is that they skip over many details.

Point 1:
Since scientists learned how to "read" the whole genome in the 1990s, they discovered a large percentage of species' genes are not related to any other lineage. At first they thought the lineages would fill in as they did more sequencing, but they eventually realized the genes did not all follow the neo-Darwinian theory. These particular ones are called Orphan, or ORFan, genes. The Orphans show up at a rate of at least 10-30% in all lineages. Wikipedia has an article about Orphans HERE. (If you read this or any other article about biology, beware that the evolution theory is usually assumed as proven. So just try to get the actual facts.) The abstract of this artice by Arendsee, Li and Wurtele, "Coming of Age: orphan genes in plants," Trends in Plant Science 19, 11 (Nov. 2014): 698-708, also speaks of orphans in all species.

Point 2:
So because Orphans became part of the overall picture, scientists are looking for other ways to justify evolution. Before, they said small mutations in genes over billions of years would bring the changes we see in species and beyond, all through life's varieties. So now they are telling us the reasons genes are not following trees is that various major mutations and duplications can happen within the non-functional part of the genome, or they go from one species to another by what is called horizontal gene transfer (HGT). I will take HGT under Point 3.

But experiments over the last 30 years have shown that functional proteins are very rare. Among the papers describing this rarity 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. When similar experimental results are considered, we can use the proportion of 1 in 10^70 as a guideline for function of a simple protein "fold." Folds are the parts of proteins which react with other biochemicals to process our metabolism.

It has been estimated that less than 10^50 organisms could have been alive on Earth.  This was done, among others, by Fredric P. Nelson, “Needed: A New Vocabulary for Understanding Evolution,”  Perspectives on Science and Christian Faith 58, 1 (March 2006): 28-36.

Bacteria have less than one mutation per generation. Even in billions of years, there were not enough organisms to bring about millions of unique, Orphan genes to functional structure (there are estimated to be about 10 million species on Earth). This is not even to mention the continuing discoveries that more of the "non-functional" part of the DNA is in fact useful for a variety of reasons and probably not available for mutation.

Point 3
Horizontal gene transfer is an exchange of DNA between species. The sets of proteins used in HGT, along with other functions,including the secretion of toxins, are know as "secretion systems." There are various types, and I have images of one part of a Type II and full Type IVa machine. There are good images and information of both of these systems online in a scientific article by Chen and Dubnau, "DNA uptake during bacterial transformation," Nature Reviews Microbiology 2, 3 (April 2004): 241-249.

Information about this process has been studied and the following facts are from an article by Thomas and Nielsen, "Mechanisms of, and barriers to, horizontal gene transfer between bacteria," Nature Reviews Microbiology 3, 9 (October 2005): 711-721. Although HGT does work at the single-celled organism level, most changes are deleterious. Of the few that do persevere and spread, they are most often involved in simpler biochemical pathways, even in antibiotic resistance. They do not affect the most central workings of the cell, such as DNA replication. Even so, it takes about 20-50 already functional, coordinated proteins to perform HGT.

Scientists and others have used these systems as examples of evolutionary sources for the bacterial flagellum system, which in turn is a model of design given by Intelligent Design advocates. But the anti-design scientists don't explain how the proteins of these systems arose and organized into working machines of their own.

Type II Secretion System

The first image is one protein of a Type II secretion system. It is from the work of Abendroth et al., "The X-ray Structure of the Type II Secretion System Complex Formed by by the N-terminal Domain of EpsE and the Cytoplasmic Domain of EpsL of Vibrio cholerae," Journal of Molecular Biology 348, 4 (May 13, 2005): 845-855. The protein is called Cyto-Epsi," and the PubMed Abstract in part describes it:

Gram-negative bacteria use type II secretion systems for the transport of virulence factors and hydrolytic enzymes through the outer membrane. These sophisticated multi-protein complexes reach from the pore in the outer membrane via the pseudopilins in the periplasm and a multi-protein inner-membrane sub-complex, to an ATPase in the cytoplasm.

The image shows a protein that has one type of chain with 254 amino acids, but it is a 2-mer, which means there are two of the same type in the molecule, totaling 408 amino acids. Amino acids are the subunits of proteins and have an average of about 20 atoms. The double chains of the 2-mer are apparent from the mirror-type image. Remember, this is just part of the system.

More information, including the journal abstract, about Cyto-Epsi from Type II can be found at RCSB PDB 1YF5.

More information on Type II secretion systems at Wikipedia HERE.

Type IVa Secretion System

The second image is a Type IVa secretion system (piliated, which means the center has a separate protein string that the system made). The journal article which describes this is by Chang, et al., "Architectural model of the type IVa pilus machine," Science 351, 6278 (March 11, 2016): aad2001. The full Science article is online with images at the link in the title.

This image of the Type IVa Pilus Machine is from Uniprot, another protein database. It is pictured at the links to the individual proteins that make up the machine. For example, one of the proteins is called PilB, and when you go to Uniprot PilB entry (with the right browser setup) you get this image. It is under the heading "Structure" and you can even manipulate the 3-D image! Give it a try at PilB entry Q1D098. Once again, this machine is not the whole system.

More information about the Type IVa pilus machine is at RCSB PDB 3JC8.

At the RCSB PDB 3JC8 link, there are Protein Feature view charts for each of the 9 types of proteins that make up this particular machine. The third image here is the Type IVa pilus assembly protein ATPase PilB from the organism, Myxococcus xanthus (strain DK 1622). The 9 types of proteins (entities) have multiple chains of each. In this example, PilB has 566 amino acids in each of 6 chains (the blue lines).

The amino acid sequence of PilB is what each of the blue lines represent. This particular one is shown here from the Uniprot website, each letter standing for a specific amino acid:

The total amino acids (also called residues) for this machine are listed at the site as: 37,468. Total atoms: 107,640. All have to interact in size, shape and charges for the machine to be in working order.

More on Type IV Secretion Systems at Wikipedia HERE.

If you've gotten to this point, thanks for following along. I hope you see these systems are themselves intricate, not easily explained away.

Combinations and Permutations

The title of this post should add "and Probabilities," but I think that would have too many letters. The numbers of possible combinations and permutations of things also are related to their probabilities of taking place. These subjects are in turn tied to the possibility of totally materialistic evolution.

We should not argue about all or none evolution. Some proteins can lead to some changes in organisms. But that does not cover the whole story. I see those who say they haven’t seen any evidence against materialistic evolution. But it is very much available in scientific articles in peer-reviewed journals. There are also those who say evolution is established. That is only in part.

It can be difficult for people to understand vast numbers involved and also the chemistry of proteins because they are admittedly complicated (and I am no expert but I think I have the relevant concepts). Also, when we use examples, like card games, we must be careful and try to get down to the bottom of the truth. Metaphors and analogies can be helpful but they only go so far and can even be misleading.

To begin, the terms “Combinations” and “Permutations” are different and are calculated differently. There is an explanation of the different formulas for figuring 4 kinds of combinations and permutations on the web page by Rod Pierce, "Combinations and Permutations," Math is Fun, Advanced, Sept. 30, 2018 (citation below). Combinations do not require a specific order of possible items or units. Permutations do require a specific order. Both are also defined by whether repetition of units is allowed or not allowed. All of these are calculated differently and bring very different answers. 

The Math is Fun website uses the letters “n” and “r” to denote the number of types of a “thing” and number of the things chosen, respectively. The author then shows how these symbols are used in different equations. In an example about proteins I will explain below, one term is n^r. The ^ symbol stands for a caret which is used to denote an exponent. The exponent, in this case “r”, tells you how many times to multiply the base, in this case “n”, times itself to get the answer. 

Many think of cards when it comes to probabilities. In a deck of cards, there are 52 different kinds, such as the Ace of Diamonds, but only one of each is available in figuring number of combinations of each hand. If there is only one deck used, there is no repetition of each of these kinds. The individual poker hand is smaller yet--only, for example, 5 cards. Also, the order in which you draw the cards does not matter. For a Royal Flush, you don't have to draw the Ace first, King second, etc. 

In this case, you will run into another symbol, the “!”, known as the factorial function. It means that you multiply a number times all the next whole descending numbers, such as: 5! = 5 x 4 x 3 x 2 x 1 = 120. The formula to find the number of possible 5-card poker hands is n! / r! (n-r)!. That’s n! divided by r! times (n-r)! where n is 52, the total number of cards, and r is 5, the number that is chosen. The number of 5-card hands for a 52-card deck is 2,598,960, or about 2.6 x 10^6. (The Math is Fun site uses billiard balls but the category is the same.) Probability is related to these possible numbers which I will discuss below.

Now, a functional protein, which is made up of units called amino acids, is usually longer than 100 units. Some have thousands depending on which function they have. There are 20 types of amino acids in biological life. The function of proteins depends on the chemistry of each of these amino acids and how they interact with each other. In talking about the probabilities of these amino acids, we don’t even get into the chemistry of how they might avoid interacting with other types of molecules. So at this very basic level, an important point to make is that there can be any number of each of the 20 kinds of amino acids in the proteins. Therefore, repetition is allowed in this case and therefore must be part of the calculation of the number of possible permutations. Order of the amino acids is of primary importance if you want the protein to work. Therefore order must be part of the calculation of the number of potential permutations. When repetition is allowed and order matters, the formula is n^r, the example given above. For a protein of 100 amino acids, that would be about 20^100 possible permutations, or 10^130 in base 10. In contrast, the estimate of the number of particles in the universe is 10^90, and seconds in 14 billion years about 4.4 x 10^17.

It may seem that getting a functional protein would be easy with this amount of permutations. But that is where probability comes in. Probability is closely related to the inverse of combinations and permutations. In general, probability of an event equals the number of ways an event can happen divided by the number of total possible outcomes. For example, a die has 6 total possible outcomes but only 1 actual outcome per event. Each event (tossing the die) would have the probability of 1 divided by 6, or 1 in 6.  If you have 8 marbles in a bag and 6 are blue and 2 red, your chance for picking a red one are 2 divided by 8, or 1 in 4. In poker, the Royal Flush is the most rare hand, an Ace, King, Queen, Jack and 10 of the same suit. There are 4 ways this event can happen of the 2,598,960 possible outcomes, giving a probability of 1 in 649,740 (about 1 in 6.5 x 10^5). A lot of people play poker throughout the world, so the event does happen every so often. More information on probability can be found at Wikipedia HERE.

With proteins of 100 amino acids, the total number of possible permutations is approx. 10^130. In an increasing number of experiments on proportion of protein function the number of amino acids per examined protein has been around 100, with functional protein outcomes in the realm of 10^60. This is admittedly a very high number. But the probability that 1 of those outcomes would be selected is 10^60 divided by 10^130, which equals 1 in 10^70.

The experiments for protein rarity have focused on the function of simple folds. The probability of complete, large proteins would be smaller. The maximum number of individuals that could have lived on Earth even in 4 billion years is 10^50, which limits the number of "tries" for functional proteins. With bacteria there is less than 1 mutation per generation and with humans less than 10^2. Probabilities are used in science such as chemistry. It is reasonable to see these scientific discoveries as evidence against materialistic origins and evolution of life. The implications of these numbers are further developed in my recent blog post “Important Research.” 

The citation for the Math is Fun page is:

Pierce, Rod. "Combinations and Permutations" Math Is Fun. Ed. Rod Pierce. 30 Sep 2018. 13 Jan 2020 <http://www.mathsisfun.com/combinatorics/combinations-permutations.html>

Praise God for Creating DNA

Way back in January 2013, I did a post about the make-up of a part of the cell which produces energy, a set of proteins called ATP Synthase. The post is HERE, and it includes a little video about ATP Synthase which processes protons through a membrane due to an electrical gradient set up by yet other sets of proteins. I want to re-post a picture of this sequence from KEGG database called "oxidative phosphorylation" because it is amazing (sorry if my reproduction is a little fuzzy-- a direct link for this image data is HERE). Please note that all the different-colored parts are different proteins that have different genes:

However, I did not add everything I could have to that post to make the picture complete. I showed the amino acid sequence of one of the sub-unit proteins, but I'd like to take the composition of a Beta sub-unit one step further to show the human gene sequence. This is the darker blue piece of the protein set on the right of the above picture:

Each letter in the image above stands for a molecule called a nucleotide. These in turn are a code for producing the sequence of amino acids needed to make the protein subunit. In this case there are 1590 of the DNA nucleotides. These molecules, made of atoms, exist in the ladder-like DNA helix structure which sends a code through the cell to make proteins. There are 4 letters in the chart above --c, t, g and a. Below is a picture of them (the fifth, Uracil, is in RNA, a whole other story). The N stands for nitrogen, H for hydrogen, O for oxygen, and C, carbon, is understood in the corners of the "rings" that don't have letters). The R is where they attach to the rest of the DNA molecule:

Though perhaps every amino acid (coded by the DNA nucleotides) does not have to be exactly where it is in this Beta subunit, as in all proteins, many do. The protein has to have a structure that will hold together in a certain shape, and some amino acids do better on the outside of the protein and some on the inside. Then this Beta piece along with another type of protein provide the conformations that allow the chemical change of one molecule into another (ADP to ATP). The ATP is what gives energy to our metabolism and in fact is needed to produce more DNA and proteins. The machine-like quality of the ATP Synthase is due to several specific amino acids that can accomplish this task when the ATP Synthase complex turns on an axis. There is another way to produce ATP which I won't go into: substrate-level phosphorylation. This requires its own complex sets of proteins and you can always Google the name if you are interested in learning more.

Overall, you have a chicken and egg problem: DNA is needed to code for the proteins that make ATP which is needed to make DNA. Though many want to believe that life came through natural physical laws, we have to consider at least two events: first, beginning of life; second, continuation and change of life forms (evolution). At the beginning we have to understand that the chemistry that would affect the atoms of the atmosphere is under the Law of Mass Action (Wikipedia entry HERE), where atoms and molecules move randomly but collectively act in a certain way. Even quantum physics becomes random at the Newtonian level. Though some want to dream of finding physical laws that would put DNA together "naturally," in my opinion they are literally dreaming. They accuse Creationists of not being able to acknowledge that God could create through physical laws, but what about them acknowledging that He could create directly?

In the Bible, the Apostle Paul says that God made Creation in a way that it is obvious for us to see His eternal power and divine nature (cf. Romans 1:20 NABRE). I agree with Paul.

Praise God for His Creation

I went to the Farmer's Market yesterday. Our town has a great FM, and this time of year it is full of produce, but also showing signs of the impending autumn. There are gourds and Chrysanthemums, and also one of my favorite flowers, Gladiolas (they are late in Michigan). I have a picture of one here, admittedly from the Internet under free images of flowers. One of the reasons I am writing this is to praise God for His creation, something I don't think we do enough. Perhaps it is "understood" that if we look at flowers and believe in the Lord, that we admire His handiwork. But I'd like to hear more of "Praise God through Jesus Christ for His Creation."

That is why I have the idea to make a thread at the Catholic website Catholic Answers Forums (CAF) that says that or something similar. But before I do that I have to get some things done, like getting my nook charged up for the first time and, as I understand it, sign in to places I've registered already such as Google. I've been putting it off but I'll be going back to my mother soon for her to have more surgery and I'd like to have my new nook there so I can read the books I have on it (I guess the ones that are on the previous one are carried over to the new one). There are other things going on too, such as trying to finish editing and re-writing my first book, Mission: Faithful, so I can put it here on my blog.

Another thing is that I would like at CAF to take the Creation part down to the molecular level, to show how the Lord has used His mighty creativity to get the biological world working in the first place. We will see how it all goes.

Undeniable by Axe

I just read the book by Dr. Douglas Axe, Undeniable (HarperCollins Publishers, 2016). The subtitle for the book is: How Biology Confirms Our Intuition That Life Is Designed. Dr. Axe is a biology researcher who started in engineering and went on to study the working molecules of our cells, especially proteins. I’d like to mention a few things about it because even though it is written for the non-scientist it might still stand a few more comments. Proteins are not often described to the general public but he does a great job.

The Intelligent Design (ID) movement will celebrate its 20 year anniversary this August, and Dr. Axe is among its advocates. ID advocates claim that design can be detected in biology by using strictly scientific methods. However, for the scientist working in research who talks about biological design, there is awkwardness among his/her colleagues which can lead to total exclusion. Though Dr. Axe worked at extremely prestigious institutions such as Cal Tech and Cambridge, he was intimidated and even ostracized when he shared his new ideas.

Dr. Axe doubted the scientific consensus of his day that said that proteins are easily made by chance. Proteins are specific molecules that do specific jobs in the basic unit of our bodies, the cells. Axe believed they have to be very fine-tuned in order to fold into the shapes they need to be to carry out their work. One of the best parts of this book is that Dr. Axe has drawings and descriptions of proteins. These molecules have to be seen to be appreciated and the more the general population is aware of these structures, the better. I was especially happy he described the proteins of photosynthesis, since this is one of the most crucial processes of life because it converts light energy to food. The machinery for photosynthesis would have had to come about in some way.

Good a job as he did, the book was in black and white and I'd like to put in one color picture of what he had.  Also, I'd like to show structures of the sub-units of protein, called amino acids and the atoms which make them. This is a worthwhile description to give people more of a grounding of where the proteins fall in the nature of things.

We’ll start with a protein complex Dr. Axe does describe, a molecular machine of photosynthesis called Photosystem I. This molecule takes in photons from the sun which eventually fixes carbon into the building blocks of the cell. Keep in mind this is only one of several molecule complexes needed for photosynthesis to occur. These in turn set up electrochemical gradients and molecular products the cell needs for building the vast array of machinery it has.

Dr. Axe shows different parts of Photosystem I in his book, although the pictures there are in black and white. I have a color picture of the whole thing from the National Center for Biotechnology Information entry 1JB0 (citations at bottom of image). Dr. Axe tells us there are 417 parts to the Photosystem I complex (many kinds are used more than once). In this first stunning picture, different parts are marked with different colors. Not all the parts are proteins, but most of what you see are (sub-parts of helices, strands and coils).

The next image shows all the amino acids needed to make up just one protein of the 36 total (12 kinds) for Photosystem I. This analysis is from a cyanobacterium, a single-celled organism. The abbreviations are for the 20 different amino acids, which we will get to next. The information is from Uniprot entry P0A405.

Then, I have a picture of an amino acid here with the atoms of carbon, oxygen, nitrogen and hydrogen (the abbreviations may be the same for amino acids but are known because of context). In this example is the amino acid valine (rhymes with way lean). The amino acids are partly all the same (on the top in this picture) where they combine to make a protein chain and differ (on the bottom) in their “side-chains.” These side-chains give the proteins different structures to do different jobs. The amino acids have an average of almost 20 atoms each.

Then in my last image I show the perspective of the first three images and what it takes to make up just one of the parts of Photosystem I (in the top circle) with the 755 amino acid abbreviations listed. Valine is marked by a V in each space it appears. This piece would have about 14,000 atoms—all in specific order so the larger machine can work as it should.

In the book, Dr. Axe spent a lot of time describing the possible number of images in a pixel grid using the three basic colors and all their intensities in order to describe the huge “search space” to get one specific image out of all the possibilities. It is similar to saying that we “try” a certain amount of times putting different combinations together to get what we want.

The structures for photosynthesis are amazing in the number of their amino acids and other molecules which combine for the work of photosynthesis. It would take a tremendous amount of chemical reaction “tries” to get the right atoms in the right positions under random conditions. Dr. Axe gave the idea of how large the search space is for specific proteins. We are talking about one in 10 to the power of 74 (10^74), which is a one with 74 zeroes after it, for a proteins of 150 amino acids. In a comparison, this is less than one atom in all the atoms in our galaxy. Even with the large amount of atoms to work with and even in an old Earth, we can consider the random combinations of atoms to be insufficient to put together the structures needed for photosynthesis. And it could not have happened piecemeal, because you need the whole system for photosynthesis to work.

Lastly, I want to say that in his book Dr. Axe takes a diversion from the regular ID advocates and names God as the Designer. Others in the ID world say they are only looking at the science of biology, and conclude it is designed without naming the designer. I am wondering how the other advocates will handle this conclusion, since their critics have always accused them of being Creationists underneath all the claims of science-only. But I am glad he did it, because I think all ID advocates should be up front about who they think the Designer is.

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.

Supernatural Creation

I believe that Creation has had direct supernatural intervention (called Special Creation), both at the beginning of life and along the way from simple organisms to human beings. I don’t know if the “days” mentioned in Genesis 1-2 lasted 24 hours or were long ages, but I believe there was a direct supernatural element in the formation of humans.

So why do I believe this? I have a tendency to think of biology. With biology there are vast numbers to consider. The first in this vein is the number of our cells, the basic unit of biology. I’ve seen estimates that humans have about 10 to 100 trillion cells, all working together. How big is a trillion? A trillion is one million (already a big number) times one thousand times another thousand. So take all that times 10 to 100 and you have the number of cells of an adult human being. We’ll say 50 trillion as a rounded number for discussion. Understandable information on the cell is at CreationWiki under Cell Biology HERE.

These 50 trillion cells all start with one cell from union of a sperm (from the male) and an egg (from the female) that meet through sexual intercourse. Now this first cell is already a wonder. It contains molecules inside—made of atoms which combine in specific ways. A central molecule is DNA, which is in the form of a code to make other molecules. DNA looks like a ladder twisted along its long axis and the steps or rungs are composed of smaller molecules that follow a precise order. Parts of the DNA are known as "genes." More information and pictures of DNA are at CreationWiki HERE.

At specific times, these rungs separate in the middle and are copied for the code in order to make other working molecules and more cells. The rungs of the ladder, more officially known as “bases,” in the human number 3.2 billion in each cell. Yet the average cell is only about 10 to 100 microns long. This equals about 1/250th to 1/2500th of an inch long.

So 3.2 billion DNA bases (the rungs) are active in almost all new cells that come from the division of the first cell and the next and the next etc. The DNA has to be copied in the right way for differentiation into the right kind of cells as they come about during the divisions. The cell products have the effect of making the right cells for eyes, ears, nose, bones, muscles, inner organs, skin, and everything else that makes our physical bodies.

The organization of the growing human in the womb, baby, child and adult must be regulated by genes which are made up by the DNA. Some regulation comes from the DNA and some from the egg cell to form the body orientation.

All the while, cells need to be able to use food to make the right kind of energy for them to keep growing and dividing. As mentioned before, the DNA has genes, and these make proteins that do the work of the cell, such as copying DNA and digesting food molecules.

These are among the facts that make me believe humans needed direct supernatural intervention in our formation. I hope you will consider these numbers too. Don’t let others tell you they would be easy to come about. Neo-Darwinian evolution involves chance—just atoms that happen to come together with no guidance. Though evolutionists invoke natural selection of the fittest, there has to be something from which to select if you are to have neo-Darwinian evolution at all.

I don't believe the original DNA sequences needed for life came about by chance. I don't think we'd have the tiniest cell, much less a human, if it were not for the direct intervention of God.

Creationists and IDists v. BioLogos

This post is a little complicated, but it is important concerning the "evolution wars," and I've edited a few times to make it as clear as I can. To start, BioLogos is a group of people who are committed to "Theistic Evolution" (TE). TE is the premise that animals and humans developed by evolution helped along by God. Theoretically this help could come directly, such as if He intervened in the genes of an embryo to be therefore born slightly different than its parents. This approach does have the problem of people coming from animals. Or, in the version pushed by BioLogos, God could have acted in a Divine Hands-off manner (also known as Deism). This scenario supposes that God somehow caused evolution to happen in a pre-planned way that would LOOK to us as random.

There are several problems with this Deism view. One problem is that on a physical level it correlates exactly with any secular or atheist’s view of evolution, what we call neo-Darwinian evolution. Secularists look at evolution as random (the random genetic mutation element means the basis of evolution is random even though there is a non-random element called selection). Another problem with this view is that there is a logical fallacy in saying life LOOKS LIKE it was brought about in a random way because biological structures do NOT LOOK random. Our bodies have trillions of cells working together to give us life. A cell is a basic unit of biology. Proteins, which are the working molecules of the cell, are very specifically constructed for what they do. The DNA inside the cell acts as a code to make the proteins, and therefore must also be very specific. These molecules do not look random.

So we have a group of people (BioLogos), many of whom are scientists, who tell us God somehow created animals and plants and people, but we are supposed to go by the book of all secularist and atheist scientists. In contrast there are other groups of people who are actively questioning the secular view and secular-like TE view put forth by BioLogos. One group of Intelligent Design (ID) advocates is called the Discovery Institute. These people are dedicated, among other things, to make the facts known about proteins and other biological structures and claim these structures were designed. They are using scientific methods, such as information theory, to try to prove what they are saying. Other groups are Special Creationists (believing in direct supernatural creation by God), such as Answers in Genesis and the Institute for Creation Research. These also have scientists in their ranks and are using their websites to argue their cases.

Since BioLogos backs atheistic outlooks on creation and evolution, the arguments of the Discovery Institute and Creationists are directed against both Biologos and atheists. On the Discovery Institute’s newsletter website and his own, Darwin's God, Dr. Cornelius Hunter is showing why the BioLogos arguments are wrong. A very good example is in the post "Shared Errors: BioLogos on broken genes," Darwin's God (May 31, 2016).

So a major problem with BioLogos is though they say they want to show how science and religion can be reconciled, they promote both a non-religious and non-scientific (illogical) view of evolution. They imply that God is not really needed because evolution is random anyway, and that if you want to believe in God, you still better believe in non-divine-type evolution.

The person who started BioLogos, Dr. Francis Collins, a self-professed Christian, has been instrumental in the present legal status of using human embryos in scientific research. Though the BioLogos people profess to be Christian, neo-Darwinian evolution has been the only option until recently for atheists (for a new alternative, see The Third Way of Evolution).

Casey Luskin, who worked for Discovery Institute for many years, has published a paper about the relationship between atheism and the teaching of evolution. It is Casey Luskin, "Darwin's Poisoned Tree," Trinity Law Review 21, 1 (Fall 2015): 130-233. You can find the paper description and link to a PDF file at the link in the title.

It is not unusual for Christians to be right about some things and wrong about others. This is part of growth and learning. BioLogos Christians are wrong to push their random evolution agenda. Somehow they are blinded, perhaps by some imagined promise of scientific discovery, to the amazing design in biology that is obviously seen by others as supernatural creation. Refer to the Bible in resisting intimidation by scientists who tell you we came about by chance:

Ever since the creation of the world, his invisible attributes of eternal power and divinity have been able to be understood and perceived in what he has made. As a result, they have no excuse (Romans 1:20 NABRE).

Smallest Cell

An interesting discovery from the J. Craig Venter Institute is reported by Rachel Feltman, "This man-made cell has the smallest genome ever — but a third of its genes are a mystery," Washington Post, March 25, 2016. The article describes the smallest cell genome to which the scientists were able to reduce, and it turns out it is twice as big as they thought it would be.

DNA is the molecule that forms our genes. These are used for coding proteins, which do the work of our cells. Cells are the basic unit of biology and its complete set of genes is the genome. DNA is also needed for reproduction, to pass the information to offspring.

Humans have trillions of cells, and most of them contain their own set of DNA. Some organisms, like bacteria, have only one cell, but still need DNA to make protein and for reproduction. As you have probably seen portrayed somewhere, DNA looks like a twisted ladder. Each step of the ladder has a smaller molecule that acts, in sequence with the other steps, as a code for the protein so it can be made correctly. There are 4 types of steps which are called bases and in bacteria it takes about 1000 bases per gene. And as the WP article points out, “to build a DNA code that will support life, you need to be pretty much error-free.” More information on DNA can be found at the CreationWiki entry HERE.

Scientists have been trying to determine what is the least number of genes a single cell, such as a bacterium, can have and still stay alive. This is not a fully-functional cell in the sense it would have to be given nutrients that it could not produce itself. Scientists had thought the number would be in the vicinity of 250, but have found, at least in this approach, that more genes are needed than they thought. They came up with 473 and were surprised they could not find the function of 32% of them. The organism needs over 531,000 base pairs in order for it to keep "working."

An abstract of the actual scientific paper is Hutchison III et al., "Design and synthesis of a minimal bacterial genome," Science 351, 6280 (March 25, 2016).

Eugene Koonin, the director of comparative genetics at NIH, estimated a fully functional cell would need about 1000 genes. These would be fully self-functional, not needing supplements fed to them. At 1000 bases per gene, that would be one million bases in exact order. The article which contains his estimate can be found here in Koonin, Wolf, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research, 36, 21 (Dec. 1, 2008): 6688-6719.

What are the chances that even half of that, an exact sequence of 500,000 bases, could have randomly come together to start life, composing a complete genome which codes for life processes (even if there were nutrients in the environment) such as breakdown of sugar to make the structures of the proteins, reproduction and other functions, and organize all of it in tiny cells? This could not have happened by chance even in billions of years.

Praise God through Jesus Christ for His Creation.

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.

Orphan Genes

Scientists started comparing whole genome sequences of various species in the 1990’s. Genes that are only found in one or very closely related species are called unique, de novo, ORFan or orphan genes. The amazing thing is that the more they compare species, the more unique genes they find. These genes make up about 10-20% of each organism’s whole set, percentages given by Dr. Ann Gauger, "Orphan Genes: A Guide for the Perplexed," Evolution News, July 30, 2013. I have seen research even in the 30% range. These unique genes are so different from each other that the chance they could have come from an evolutionary sequence is vanishingly small. This is, for one reason, because there could have been no more than 10^50 organisms on Earth so far even if the Earth is very old. The unique genes are statistically so far apart that even this many organisms are not enough to sort through the various possibilities.  (And only one in about 10^70 proteins is functional. So the sorting of proteins for functional ones makes evolution by chance look pretty much impossible.) In contrast, if all genes (and corresponding proteins) were closely related and in obvious sequence in species, Darwin would have been proven right.

Eugene Koonin is Senior Investigator of comparative genomics at National Center for Biotechnology Information (NCBI, a division of NIH) and has written many articles. So he is on the front lines of comparative genomics. He and Yuri Wolf wrote an article in 2008: Koonin and Wolf,  "Genomics of bacteria and archaea: emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 1 2008): 6688-6719. They found there were some proteins common to many species of bacteria and archaea (one-celled organisms different from bacteria). But what surprised them was the vast amount of variety between species and the unique genes. Koonin has become part of a movement to find other explanations for evolution instead of neo-Darwinism called the Third Way of Evolution. The "evolution" part is because Koonin is committed to evolution although his move shows that he believes neo-Darwinian evolution is falsified. But these findings of comparative genomics also support direct creation of species.

Another article by J. Muller, et al., "eggNOG v2.0," Nucleic Acids Research, Database Issue 38 (Jan. 2010): D190-D195, compares various species. In the diagram there are species names in the middle with radiating lines that go out to colors of the graph. The green and orange represent genes which are related, but the outer gray areas are orphan genes which do not match other species (much easier to see in the full article at the title link).

A more recent article by Jorge Ruiz-Orera, et al., "Origins of de novo genes in human and chimpanzee," PLOS Genetics, Dec. 1, 2015, has reinforced these findings. The researcher and his group were looking for unique human and chimpanzee genes and found them. Their author summary starts:

For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species.

Homologues are related genes. As stated above, these unique genes cannot be explained by the supposed machines of evolution: mutation and selection. The complete published paper can be found at the title link.

On a related subject, a problem in the past was that in comparing genes, scientists used genes they already had to see if they were in the other organisms. This left sequences that did not match out of the loop of potential genes. However, they have begun to use other criteria, such as start and stop sequences, to now identify more non-matching areas that look like genes. This is promising to show even more unique genes.

A Matter of Faith

This month a movie that comes out on October 17 and will be showing in Grand Rapids is A Matter of Faith (Five & Two Pictures, Cristiano Film Group, 2014) which I’ll abbreviate AMOF. In it, a young woman attends college and is influenced away from faith by her evolutionist biology professor. Her father becomes upset and ends up debating the professor.

I heard a producer of the film being interviewed on a Christian radio show I listen to on Saturday mornings, and I looked the movie up on the Internet. I found the website and played the trailer (at the link on the movie's name above). To my surprise, I saw the campus of one of my alma maters—Aquinas College in Grand Rapids! I did a search and found the co-producers, the Christiano brothers of Christiano Film Group, are from Grand Rapids and the production was headquartered at Cornerstone College which is located on the East Belt Line there. Scenes were indeed taken from Grand Rapids locations including Aquinas. These facts and more were reported by Terry DeBoer in "Feature film 'A Matter of Faith' continues filming in Grand Rapids...," MLive, June 24, 2013.

I attended Aquinas College for a certificate in theology, which I received after 18 credit hours. I had already earned a veterinary degree, but have been interested in theology and spirituality for a long time. Then, around the time I was going at Aquinas, I started reading the works of Intelligent Design (ID) advocates such as Michael Behe (Darwin’s Black Box), William Dembski  (Intelligent Design) and Phillip Johnson (Darwin on Trial). I already was convinced that biological life was not a product of totally natural evolution, but I enjoyed reading their works and learning more about the controversy.

I didn’t agree, though, with the Intelligent Design advocates in their approach to science. They wanted to prove design in a strictly scientific way, but I think that faith comes first. Of course, not everyone believes. But, IF a person believes in God, THEN s/he believes all things are Created and therefore all things are designed. You don’t prove design, you believe it. However, if you want to look at the scientific part of why totally natural evolution should not be considered feasible with the knowledge of natural laws as they are now, it’s as simple as this: the complexity of biology defies probabilities.

I wish I had bookmarked a conversation I saw recently, I’m pretty sure from Evolution News, between an ID advocate and an evolutionist. I can’t find the article now, but the background is that, as scientists compare the proteins of different species, they try to match the sequences of their sub-units. If they match, the scientists say it proves that one species came from another. As I remember, the ID advocate, who wrote the article, asked how evolutionists can think that the low probability of matching protein sub-units in various species proves evolution whereas the overall probability of the proteins existing in the first place is much smaller by far. The evolutionist said something like: the comparison of proteins gives scientists frames of reference, but the origin has no frame of reference. Apparently chemistry, physics and mathematics don’t count as frames of reference when it comes to origin of life and new proteins along the way of species differentiation. Actually, the experimentally proven extreme rarity of functional proteins among all the combinations of their sub-units (amino acids) provides a very fundamental frame of reference. (The evolutionist also did not explain why the differences in proteins do not count in the determination of proof but only the similarities.)

The comparison of proteins can be accessed on the Internet in various databases. The UniRef database is from the UniProt consortium, which is a combination of particular European and American protein database providers. UniRef shows relationships between proteins in over 200,000 species. The species are classified by "taxonomy," and the National Center for Biotechnology Information (NCBI) home web page for this database is HERE. This is about 10% of all formally described species. They identify each protein and give it a cluster identification, then compare proteins to different species. If the proteins are similar, they are put together in a category of "cluster members." The charts on the database give the number of clusters that compare closely to others, along with the species names. And yet as of October 3, 2014, there are more than 7,750,000 single clusters of proteins that match less than 50% to other clusters out of a total of around 82,000,000 clusters. (2020 Update: it appears now that if there are no matches the protein is called 100% match with itself in a cluster of 1 member. An example, UniRef100_A0A001)

I took one of the clusters (UniRef entry M0E4M2) and looked a little more closely at it. There were several species in this cluster, but the group for the "cluster" were still close cousins. The protein is called “histidine kinase” (UniProt entry M0E4M2) and it is in the organism "Halorubrum saccharovorum," part of a family of archaea (pronounced are-KEY-ah). Archaea are single-celled organisms that were first thought to be ancestors of bacteria, but were found to not be related once the genes could be sequenced (starting in the mid-nineties). So this particular protein structure is so far only found in one family of one type of organism. The protein is involved in sending molecular-level signals. (Histidine is an amino acid, Wikipedia entry HERE, and a kinase is an enzyme, Wikipedia HERE).

It can be hard to get an image of a specific protein since there are so many proteins--not all have been depicted. I apologize that I have not been able to find an image of this particular one, but think I am still able to demonstrate how different proteins can look and how different their structures are. The first image is from an Archaea species, Methanocaldococcus jannaschii, of a kinase that has histidine as an active site. It is called Isopentenyl phosphate kinase, UniProt entry Q60352. The explanation of the protein is at RCSB PDB entry 3K4O.

The second image has a histidine kinase (UniProt  (Q9WZV7) from a different species known as Thermotoga maritima. This is a bacteria instead of an archaea. When the sub-units (20 different amino acids) of the Halorubrum and Thermotoga proteins are compared, the identity is figured by the ALIGN program in UniProt to be 14.2%. When I run the two proteins pictured here, from Methanocaldococcus and Thermotoga, against each other, the identity is less than 10%. And even the two Archaea proteins, from Halorubrum and Methanocaldococcus, matched only at 9.9% . You can run the Align yourself if you want by using the UniProt ID numbers of the proteins: Q9WZV7 for Thermotoga, Q60352 for Methanocaldococcus, and M0E4M2 for Halorubrum. Though they have different lengths, all with hundreds of amino acids, the matches are very minimal for any of the sections.

Some say that instead of individual amino acids, larger sections of various proteins might have randomly combined, and often you hear there is “horizontal transfer” from one species to another. But horizontal transfer depends on about 30 specific proteins, and besides the improbability of them forming in the first place, not all organisms can do this transfer. And once you get above single-celled organisms, the chances are even smaller because the transfer would have to involve the specific reproductive cells.

Even though there is a big variety of molecules throughout living systems that do similar things, this doesn't mean every protein can do every job. Just like in factories, the thousands of specialized jobs need specialized tools to do them. Or think of cars, trains and planes. Each of them are used for transportation, but you don't use car parts for a train, and train parts do not have intermediates for plane parts. Each part is made specifically for its purpose. To take the analogy a little further, there are different kinds of cars, trains and planes, and though some parts may interchange among the various types of each, many can't.

In naming clusters, UniRef compares proteins and the manual says it looks for 80% match. However, in the UniProt "Align" section, the comparison of proteins described above shows you how well short fragments match. When you get very low matches, this minimizes the idea of functional sections from different proteins somehow finding each other, at least so far. It is becoming known that about 10% to 20% of proteins of every living organism are ORFans, or those which have statistically little to do with each other (see my booklet, Creation Biology). And millions of fragments would have to unite at the exact junctures to become functional within the limit of 10^50 organisms that could have existed in 4 billion years on Earth.

All Christians should consider themselves Creationists because, as it says in our creeds, we believe God made all things, visible and invisible. Unfortunately in today’s academic atmosphere, even Christian colleges are blocking the attempts by certain Creationists called Special Creationists to make their cases. Special Creationism is a belief that God made humans and “kinds” (similar to species) directly without long-term evolution. Many Fundamentalists are Young Earth Creationists, but one can be open-minded about the age of the Earth and still believe people were created directly, in a way that they did not stem from other species.

Even Theistic Creationists, who are supposed to believe that God intervened along the way of long-term evolution, don’t seem to want to talk about the supernatural part. Many from their main think tank at Biologos seem to insist that evolution is totally materialistic and at bottom a random process.

The situation is worse in secular colleges, where the mere mention of supernatural biological Creation by God brings condemnation. But it is a shame that the Christian universities are almost as bad. From the overall situation comes the movie AMOF which, as said above, involves a college student who is being taught evolution by her biology professor. Her father is fearful she will lose her faith altogether which is why he debates the professor.

The AMOF movie does not have the wide distribution of “God’s Not Dead,” but the movie conveys very real problems felt in the Catholic world. The Catholic philosophy of “Thomism” in which St. Thomas Aquinas, the great scholar of the 13^th century set out to blend faith and reason, is very complex. But to address one point, I have heard it said in the name of Aquinas that God created the universe in a way that all things were laid out in order and that He would never contradict that natural order by intervening in a supernatural way once it was laid out.

A problem in Thomas' time was that the Greek philosophy had recently become available to European minds through its translation into Latin. And for one thing, there was an apparent conflict between this “Reason” and “Faith” over the source of the universe and its contents because the Greeks (such as Parmenides) had said “Nothing comes from nothing.” Christians believe that God made the Universe from nothing. So Aquinas held that though things are usually made from other things, there must be a “First Mover” and a “First Cause.” But he also specifically commented about the creation of humans.

In Summa Theologica, Part I, Question 92, Article 4, Thomas Aquinas says this in his answer (after laying out the contrary argument [objection] first, which is at the New Advent link HERE if you want to read it):

As was said above…the natural generation of every species is from some determinate matter. Now the matter whence man is naturally begotten is the human semen of man or woman.  Wherefore from any other matter an individual of the human species cannot naturally be generated.  Now God alone, the Author of nature, can produce an effect into existence outside the ordinary course of nature.  Therefore God alone could produce either a man from the slime of the earth, or a woman from the rib of man.

 In the next statement, Reply to Objection 1, Aquinas says: 

This argument is verified when an individual is begotten, by natural generation, from that which is like it in the same species.

 Darwin’s Theory of Evolution was causing problems for the Church, but there was philosophical upheaval before then. In 1879, Pope Leo XIII put out an encyclical called Aeterni Patris. He said that science is good, but it needs to be combined with faith, and used St. Thomas Aquinas as the ultimate model in the combination of the two.

I'll never know all the in's and out's of philosophy and theology. I do perceive we've gotten to the point where anyone who argues against neo-Darwinian theory is considered either an anti-science Fundamentalist or an anti-reason, anti-"form"ist. We are treated in a hostile manner by many Catholics as well as atheists. Well, the complexity of biology is showing that the Fundamentalists may just be right after all.

It is a little risky to speculate on what God would or wouldn’t do. Some think He’d never “trick” them by making genes “look like” they have mutated over time when they really hadn’t, such as they say is the case with Vitamin C gene. However, the Fundamentalists have long associated imperfect (fallen) nature to original sin. In fact, it would be contrary to our doctrine if nature were still perfect. But I’ve never heard this aspect discussed by the detractors.

We are left with the question of whether God created species or kinds in increments, with parents of different characteristics. Though Darwin claimed it was a slow process, in the intervening years we have found the difference in body make-ups between parent and child would have to be pretty big in some cases. Can the parent bug give birth to a fish-type child?  (I'm exaggerating, but only a little.) The body type comes from the egg as well as the DNA, so the egg would have to have major changes from within the parent. I’ve never heard any proposal of scientific-supernatural solutions for these problems from Theistic Evolutionists. Maybe I’ve just missed them, but I doubt it.

I used to accept that people come from apes, but I don’t anymore. People were made by God, and I think He did it directly and supernaturally and not by evolution. I am not saying God wouldn’t make people by evolution, because He does as He sees fit. But it’s just as logical to think He didn’t have a person born to an ape as that He did.