A Blessed Fourth to You

May all of us in the US have a blessed Fourth of July, with thanks to the Lord for what we have and sincere desire to do better where we fail.

May all people have the liberty that hearts long for.

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.

The Certain God in Uncertain Times

In this present COVID-19 pandemic, many are anxious.  I hope those who are Christians will be able to put their trust in the Lord, to experience optimistic emotions and perform helpful actions. We believe the Lord is in control.

If you are not a Christian and are worried about your future,  I invite you to get to know Jesus. I have written a booklet called Heaven's Passport which may help you overcome doubts. The page with a description and link is RIGHT HERE.  You can also click the picture of it in the right column of the home page for more description.

I pray for all of us to get through this challenge and be enlightened as to what is truly important.

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 the Lord in 2020!

Let us praise the Father, Son and Holy Spirit.

By God's help let us make Him known to others.

I pray for all to have a Blessed Year 2020.