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  • Writer's pictureJon Peters

Evolution: Minor Musings

Updated: Jul 2

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

Charles Darwin. On The Origin of Species


A. How to use this section

When interacting in dialog about evolution, there are major topics which deserve significant discussion. Many other topics are minor however and can probably be addressed with a short entry. This section is for those; a collection of items that often still make an appearance in debates by anti-evolutionists but can be addressed without needing a lengthy explanation. Many even are asked not to be used by a major Young Earth Creationist site.


The best way to use this section is to just enter a topic of interest into the Search Function in the upper right. There is no particular order to the entries. Also, below is a listing by topic.


B. Index By Title

11. Atheism & Communism

21. Atheism is not a religion

Cambrian Explosion (see blog here)

6. Coelacanth Fish

De Novo Genes (see blog here)

2. Dinosaur blood and soft tissue fossils

19. Earth the Center of the Universe by Cosmology?

18. Edward Blyth

ENCODE (see blog here)

22. Evolution is not a religion

10. Evolution - just a theory

12. Evolution - atheistic

19. Genesis 1:1 "In the Beginning..." - is it translated correctly?

9. Genomic Entropy

14. Incomplete Linkage Sorting

Junk DNA (see blog here)

13. Love Explained Naturally?

17. Human-Chimp DNA Similarities

4. Human & Apes?

5. Humans Did Not Evolve From Monkeys

Orphan Genes (see blog here)

New Genes, New Information (see blog here)

8. Polonium Haloes

16. "Polystrate" Fossil Trees

7. Punctuated Equilibrium

1. Second Law of Thermodynamics

23. Shapiro, Noble and The Third Way

15. Stegosaurus carving?

3. Transitional Fossils


C. Topics to Avoid

From the Young Earth Creationist organization Answers In Genesis, is a page where they have determined that some topics should no longer be used by those advocating against evolution. https://answersingenesis.org/creationism/arguments-to-avoid/


Second Law of Thermodynamics

The Fall

Darwin’s Supposed Conversion

If Humans evolved from apes, why do apes exist today?

Have NASA computers proved Joshua’s long day?

Was there no rain before the Flood? God created things to “look old”.

Didn’t Darwin call the evolution of the eye absurd?

Didn’t a fishing boat find a dead plesiosaur?

Women have more ribs than men

Darwin’s deathbed conversion - a legend?

Were giant skeletons found in the desert?

That boat-shaped rock…is it Noah’s Ark?

The “moondust” argument



D. Anti-evolutionary Musings

It is expected that this section may keep growing as more minor topics become aware to the site's author (often ones that were refuted years ago), where the main blogs and entries once written will not be significantly changed in the future.



1. The Second Law of Thermodynamics.

Claim: The 2nd Law describes increasing disorder & entropy at every energy exchange. Evolution is fundamentally an increase in order and complexity. Thus it violates the Second Law.


Response: The 2nd Law of thermodynamics only applies to a closed system. The earth is not closed but is bathed in energy from the sun. For the same reason that a developing fetus is not violating the 2nd Law as it increases from a single celled zygote to a complex organism with trillions of specialized cells. The net energy/heat must be evaluated and evolution in no way violates that. Another way of saying this is that an increase in entropy is an increase in dissipated heat into a form that can no longer do work as energy is transferred between organisms or systems. Again, only applies to closed systems.


Eventually the sun will die out and then evolution will stop on earth (yes, I know there won’t be an earth because of the way our star will die). If there could be a planet here after our sun’s death, the ultimate satisfaction of the 2nd Law and entropy increase will happen at this location. https://biologos.org/common-questions/does-thermodynamics-disprove-evolution


2. Dinosaur blood

Claim: Soft tissue has been found in dinosaur fossils supposedly 60+ millions of years old. It is impossible that soft tissue would be preserved for that long, thus dinosaur fossils must only be a few thousands of years old.


Response: Scientists never imagined that any organic material could last millions of years in fossil specimens. One researcher decided to test that in 2005 and Mary Schweitzer shocked the scientific world with the finding of collagen in an intact T. rex specimen she reported in 2006. Fourteen years later scientists finally revealed what probably was occurring. An iron oxyhydroxide mineral was probably cross linking with the proteins producing a very stable organic compound which was protected by the dense mineralized bone around it. Evolution is not threatened at all by this finding.


A 2023 published study looked at the two major hypotheses that explain how soft tissue could be fossilized for millions of years and determines that rather than being exclusionary, they both are probably part of the same process: "This review posits a chemical framework describing the persistence of biological “soft" tissues into deep time. The prior iron-mediated radical crosslinking and AGE/ALE mechanisms are re-described in context of established chemistry from a diversity of scientific fields. Significantly, this framework demonstrates the hypotheses presented by Schweitzer et al. (2014) and Wiemann et al. (2018) are, in many cases, subsequent steps of a single, unified reaction mechanism, and not separate hypotheses. Knowledge of the chemical mechanisms underlying vertebrate soft tissue preservation has direct implications for molecular archaeology and paleontology, including efforts at molecular sequence recovery within the ancient DNA and palaeoproteomic communities." A chemical framework for the preservation of fossil vertebrate cells and soft tissues https://www.sciencedirect.com/science/article/pii/S0012825223000569?via%3Dihub

Dinosaur blood and so much more! 2019. Buchanan, Scott. More: Mary Schweitzer, PhD on creation. Radiometric dating. Great Review. https://letterstocreationists.wordpress.com/dinosaur-soft-tissue/?fbclid=IwAR2r9A1n8DpdwXJXOWqYooCiDRYGOaR7rKiFww-MbgPMAW_KXeZtvOf0J3A Why radiocarbon gives erroneous dates on dinosaur bones https://online.ucpress.edu/abt/article-abstract/84/6/336/189896/Radiocarbon-in-Dinosaur-Bones-RevisitedProblems?redirectedFrom=fulltext

More troubling is when a leading anti-evolutionist and apologist makes what should be a very embarrassing video about the discovery. Please watch: https://www.youtube.com/watch?v=R9bo9tyTmC8


3. Transitional Fossils

Claim: There are no transitional fossils. Because to an anti-evolutionist evolution cannot be true and thus there can’t be any.


Response: There are scores of transitional fossils. Some like Tiktaalik were first predicted and then found by looking in the appropriate aged rocks. These fossils show an intermediate state and characteristics between an ancestral trait and those of its later descendants. Indeed the 200+ whale fossil species can all be considered transitional. See part 2 of the evolution of the whale and fossils presented here that actually shows hind limbs shrinking, blow holes migrating, intermediate whale fossils with teeth and baleen, etc. It is simply not true that there are no transitional fossils. There are plenty.


4. Humans & Apes

Claim: Humans are not apes.


Response: Sure they are. We are not plants, rocks or fungi; we are animals. And when looking at comparative DNA, anatomy, and physiology we resemble the great apes and are placed with them in taxonomy and classification.

K. Animalia>:P. Chordata>C. Mammalia>O. Primates>F. Hominidae (Gorillas, Orangutans, Chimps & Bonobos, and Humans). This generally has been the classification used in some form by science as early as 1758 by Linnaeus and especially by Gray in 1825.




5. Humans did not evolve from Monkeys

Claim: We did not evolve from monkeys. If we did, why are there still monkeys?


Response: Correct. We did not evolve from present day monkeys, but rather from a shared ancestor with them. The last ancestor we shared with chimps was about 6 million years ago as determined by DNA molecular clocks and fossils, although no fossil of this species has been found to date. The tropics rarely produce good fossilization due to the warm temperatures and degradation. In addition, we have human chromosome 2 fusion which shows why we have 46 chromosomes and the other great apes 48.


We were derived from Adam who was created from dust? Why is there still dust?

Matthew Bonnan, Malcomb Il. Middle school student evolution contestant. Florida.



6. Coelacanth fish

Claim: Science claimed that this fish was extinct. It has been found and now is called a "living fossil". It did not evolve, which disproves evolution


Response: The coelacanth's deep sea habitat has been stable over millions of years, there was little predation and there probably were few evolutionary pressures to change. Scientists thought it was extinct since until that time only fossils had been found. In 2013 it was announced that its genome had been sequenced and it was indeed evolving, although slowly. https://www.nature.com/articles/nature12027


7. Punctuated Equilibrium

Claim: There are large gaps in the fossil record. Two famous paleontologists coined the term to describe this because the gaps are persisting. The gaps are there because evolution is not true.


Response: In 1972 Eldridge and Gould suggested that the pattern often in the fossil record was not gradual change but long periods of stasis followed by relatively quick evolution, producing more of a step pattern and happening so quickly in geological time that gaps were normal. Since their publication many transitional fossils have been found. Most change in the fossil record is a mixture of stasis and gradualism. PE does not negate evolution at all. Even Darwin noted that rates of change would not be constant and probably varied between species. PE coexists with gradualism.


Hancock discusses why punctured equilibrium was eventually abandoned as a mechanism for explaining fossil record stasis. " Few concepts in the history of evolutionary biology are as misunderstood and misapplied as Gould and Eldredge's theory of punctuated equilibrium. In this video, I explain what it meant originally, the claims that it made, and ultimately why it's rejected today."




8. Polonium Haloes

Claim: Discolorations sometimes occur in rocks due to radioactive decay of alpha particles producing a dark radioactive halo looking like tiny bathtub rings on cross section. Robert Gentry spent years studying them and since polonium decays with a short half life (1380 days), these decay haloes are evidence of a young earth that was created only thousands of years ago and the basement layer is Precambrium.


Response: Although it may still be incompletely explained, enough is known that Gentry's hypothesis of a young earth creation has been refuted by Thomas A Baillieul, and others. It's basically a God of the Gaps argument. "Gentry’s polonium halo hypothesis for a young earth fails, or is inconclusive for all tests. His samples are not from “primordial” pieces of the earth’s original crust, but from rocks which have been extensively reworked. He is unable to demonstrate that concentric halos in mica are caused uniquely by alpha particles resulting from the decay of polonium isotopes. Finally, his hypothesis cannot contend with the many alternative lines of evidence that demonstrate a great age for the earth. In the end, Gentry’s young-earth proposal, based on years of measuring discoloration halos, fails to generate a scientific model that is either internally consistent or consistent with generally accepted scientific understanding of geophysical processes and earth history." [Polonium Haloes Refuted] http://www.csun.edu/~vcgeo005/baillieul.pdf


"First of all, the samples of biotite that contain Gentry's polonium halos came from pegmatite dikes and calcite vein dikes which cross-cut metamorphosed volcanic, sedimentary, and igneous rock units. The dikes are clearly the last to have formed, not the first. Second, these dikes are not the vast, extensive granite gneisses which Gentry claims are the backbone of the mountains and continents; they are relatively small features. Third, two of Gentry's sites are not even granites but calcite vein dikes, most likely of hydrothermal origin. The biotite was formed in the solid matrix by metamorphosis. And fourth, crystal size in igneous, vein, and metamorphic rocks ranges from microscopic to very large, is primarily due to cooling rates, and cannot be used to identify "created" rocks.

So, the "basement rocks" in which Gentry found his halos turn out not to be "basement rocks" at all. In fact, they appear in rocks that formed much later than Earth's oldest rocks. This fact alone tells us that the rocks bearing Gentry's halos, even if instantly created, have no bearing on the origin and age of Earth.... Still, we must give Gentry his due. Nothing in geology fully explains the apparent occurrence of the polonium halos as described by Gentry. They do remain a minor mystery in the field of physics. But this does not mean that no explanations are possible or that it is time to throw in the towel and invoke the "god of the gaps."

[Gentry's Tiny Mystery Unsupported by Geology] https://ncse.ngo/gentrys-tiny-mystery-unsupported-geology


9. "Genomic Entropy".

This is an argument developed by the creationist John C. Sanford PhD, a retired plant geneticist from Cornell University. A former atheist, he moved through Theistic Evolution to Old World Creationism eventually landing on Young Earth Creationism, a belief that rests on absurd claims like the universe and earth are less than 100,000 years old (his words), there was a global Noachian flood, an ark, a historical Adam/Eve and a "Fall", etc. He is a strong advocate of Intelligent Design, which is basically a religion and has been debunked, and even I list some examples in one of my blogs; Why not Intelligent Design? . I think it fair to see what other beliefs people hold also. What other views accompany certain assertions that they make and how does this not impact on our ability to trust their claims?


Disclaimer: I have not read his book, newest edition in 2014 at the time of this writing. The critical comments on Amazon regarding his book are telling. His basic argument is derived from population genetics modeling which is actually not his area of expertise. His background is in plant genetics as an applied geneticist, an inventor, and a good one. His basic premise is that the human genome collects so many mutations that are not removed by natural selection that if evolution were true we and other species would have degenerated into extinction long ago. He asserts that there have been no new functional genes since Adam and The Fall. Like Behe, he claims only degeneration in life in terms of structures and genomes. He dismisses beneficial mutations because they are too rare. He cites Kimera's Curve as a prediction for his conclusions. But Kimera himself disagrees with Sanford, claiming that any beneficial mutations would have a greater effect rather than none (Kimera, 1979). I don't know if Sanford is just looking at point mutations (it seems so) rather than segmental duplications and gene duplications which is how new genes are produced and has been documented - pointed out in this blog - to the level that they basically prove evolution. Population geneticists working in the field don't find Sanford's claims or other similar creationist writings for genetic entropy convincing at all. For example: "If we, as a species, were simply constantly accumulating new mutations, then one would predict the gradual degradation of every aspect of fitness over time, not just intelligence. Indeed, life could simply not be sustained over evolutionary time in the face of such genetic entropy. Fortunately (for the species, although not for all individual members), natural selection is an attentive minder. Analyses of whole-genome sequences from large numbers of individuals demonstrate an ‘excess’ of rare or very rare mutations. That is, mutations that might otherwise be expected to be at higher frequency are observed only at low frequency. The strong inference is that selection is acting, extremely efficiently, on many mutations in the population to keep them at a very low frequency.


One of the key misconceptions in the Crabtree articles is that mutations happen to ‘us’, as a species. His back-of-the-envelope calculations lead him to the following conclusions: ‘Every 20–50 generations we should sustain a mutation in one copy of one of our many ID [intellectual deficiency] genes. In the past 3000 years then (∼120 generations), each of us should have accumulated at the very least 2.5–6 mutations in ID genes’.

The loose phrasing of these sentences reveals a fundamental underlying fallacy. ‘We’ have not sustained mutations in ‘our’ intellectual deficiency (ID) genes, and ‘each of us’ has not accumulated anything over the past 3000 years, having only existed for a fraction of that time. Mutations arise in individuals, not populations. Neither does it matter that there are many thousands of genes involved in the developmental systems that generate a well-functioning human brain; selection can very effectively act, in individuals, on new mutations that impair these systems." https://www.cell.com/trends/genetics/fulltext/S0168-9525(12)00194-1


It also appears that if there is a lot of junk DNA in our genome, the mathematical modeling he uses breaks down if that is true. How we know our genome is mostly Junk DNA is discussed here. To fully evaluate his assertions one needs to know about nearly neutral theory and how it can avoid purifying natural selection to fix genes in a population via genetic drift. This approach emerges from molecular population genetics and mathematical modeling. Needless to say, we know evolution is true because of all the DNA evidence we have (see the blogs on this site). Since we and large animals have not all gone extinct, his modeling must be producing conclusions in error.


No, the universe and earth are not 6,000 to 100,000 years old and there was no ark or global Flood a few thousand years ago. Women don't die every 2 minutes in childbirth around the world due to a curse brought on by a single woman eating a forbidden fruit offered by a talking snake plucked from a magical tree planted in a middle of a fantasy garden so she would not miss it a few thousand years ago. They die and suffer because of the evolution of bipedalism and a delayed developmental process especially in infants.


Genetic Entropy is a real concept in population genetics and it's unfortunate that those writing opposing creationist claims conflate it with the 2nd Law of Thermodynamics and entropy as used in physics. Unfortunately many biologists may not be knowledgeable in nearly neutral theory in population genetics. I certainly am not qualified to discuss it. What we need is an evolutionary molecular geneticist who can actually speak to Sanford's book and this highly mathematically and specialized topic. And there is one on the Internet. No, evolution is in no way threatened by genetic entropy. It is just another creationist fail, but this one is more complicated than most and is much more "sciencey".



Genetic Entropy (Again). Mutational load paradox and more.

https://www.youtube.com/watch?v=WFoVOXeuBzg The Fatal Flaws of Genetic Entropy. Comment section instructive. https://www.youtube.com/watch?v=P2o_KC7sc98&t=1032s



10. Evolution is just a theory.

When one reads this there are at least two issues. The first is that the person does not know what a scientific theory is and secondly there is an emphasis by the claimant of "just".


Evolution is defined as the change in heritable characteristics (alleles at the DNA level) of a population through successive generations. This definition has been used in many branches of biology since the 1940s. Of course this is true - we can see it in lab experiments and also in the field directly. Evolution as it is used and studied by scientists and medical researchers is a fact. Yes, evolutionary theory is critical to modern medicine. Secondly, the Theory of Evolution is just as well supported as the scientific theories of Germ, Cell, Gravity and Relativity. We speak of the fact of gravity and also Gravitational Theory. A scientific theory is a coherent group of tested general propositions and facts shown to be correct that can be used as principles of explanation and predictions for a class of observations. It explains "how" we know the observations of evolution are true - the facts of evolution. Evolution has withstood 150 years of testing and predictions. It can be falsified. In contrast, a scientific hypothesis is an educated guess that needs testing. If we were to see smoke coming out of a internal combustion car, we could guess that it was a water leak (head gasket?) and not an oil leak by the color. Looking for the problem will confirm or rule out our educated (we know something about car engines) guess. Saying I have "theory" about the cause is not using the term as scientists use "theory", a scientific theory. At best guessing the problem causing thick smoke to come out of a car is equivalent to a hypothesis and not a theory, even though that is how we may speak commonly.


Who says evolution is both fact and a scientific theory? Lots of qualified people! "Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered." ~ Stephen J. Gould, "Evolution as Fact and Theory"; Discover, May 1981 "Let me try to make crystal clear what is established beyond reasonable doubt, and what needs further study, about evolution. Evolution as a process that has always gone on in the history of the earth can be doubted only by those who are ignorant of the evidence or are resistant to evidence, owing to emotional blocks or to plain bigotry. By contrast, the mechanisms that bring evolution about certainly need study and clarification. There are no alternatives to evolution as history that can withstand critical examination. Yet we are constantly learning new and important facts about evolutionary mechanisms." ~ Theodosius Dobzhansky. Nothing in biology makes sense except in the light of evolution. American Biology, 1983. "Today, nearly all biologists acknowledge that evolution is a fact. The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves... it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution." ~ Campbell, Biology 2nd ed. 1990. "A few words need to be said about the "theory of evolution," which most people take to mean the proposition that organisms have evolved from common ancestors. In everyday speech, "theory" often means a hypothesis or even a mere speculation. But in science, "theory" means "a statement of what are held to be the general laws, principles, or causes of something known or observed." as the Oxford English Dictionary defines it. The theory of evolution is a body of interconnected statements about natural selection and the other processes that are thought to cause evolution, just as the atomic theory of chemistry and the Newtonian theory of mechanics are bodies of statements that describe causes of chemical and physical phenomena. In contrast, the statement that organisms have descended with modifications from common ancestors--the historical reality of evolution--is not a theory. It is a fact, as fully as the fact of the earth's revolution about the sun." ~ Futuyma, Evolutionary Biology, 2nd Ed. 1986.


The Theory of Evolution is not "just" a theory. It is arguably the most important discovery made by humans. I argue for that assertion here because it affects so much of our lives - The Greatest Discovery.


11. Atheism and Communism

Claim: The official position of communistic countries about religion is state sponsored atheism. Their ideology is inherently evil and thus atheism is evil and produces immoral and dysfunctional societies.


Response: There are multiple errors with this claim. First, correlation does not equal causation. It's true that in communistic countries state sponsored atheism is often supported. That however is often a means of the communistic leaders to control religious beliefs and all other aspects of its citizen's lives. Because Hitler wore a certain type of mustache, does every man who wears a mustache believe as Hitler did?



Secondly, the problem with communist countries is not atheism but rather communism. Many of its leaders are despots and have a history of torture and killing (Stalin, Pol Pot). They did not kill in the name of atheism but rather for communism and themselves. They erected statues of themselves and basically forced worship of their leaders - which resembles a religion more than a secular society. There are no parades showing large "A" flags, no statures erected for Atheism alone.


Thirdly, this confuses atheism (see proper definition here) with a worldview. It is not. Nor is it a religion. How do we know? Because different atheists have different worldviews. If atheism was a worldview that would not be possible. What is a worldview? Compare the life of a compassionate scientist like Sagan and the evil immoral Stalin and Pol Pot. All are atheists. Does one really want to say they have the same worldview? Some atheists even have founded charities to help in disasters.


Fourth, we can test the least religious and most atheistic societies in terms of human well being and flourishing. What do we see? The best places to live year after year are the most atheistic societies, countries and in America the least religious states. See the evidence here. If one wished to compare a religious worldview with atheism, we need apples to apples and the worldview most adopted by atheists is secular humanism; that far outperforms religious worldviews - we have the evidence for that conclusion. Atheism is just the lack of a belief in theistic claims (God) due to a lack of good evidence for God assertions. It is provisional and subject to change if sound evidence is ever provided. A lack of belief can't be a belief no more than bald a hair color.


12. Evolution is atheistic

Claim: If you accept evolution, macroevolution, that means you are an atheist. Evolution always leads to atheism.


Response: Absolutely not. Evolution is a fact and theory that explains the origin of species. It makes no direct assertions about religions. In fact evolution is accepted by many believers. And this includes the Catholic Church and the Pope, leader of 1.2 billion Christians. Christian apologist evangelicals and scientists like Dennis Venema, Francis Collins, Joshua Swamidass, Denis Lamoureux and many, many others accept evolution because they realize how overwhelming the evidence is. This is called theistic evolution or evolutionary creationism (TE/EC). It is true that some religions and creationisms make assertions to history, science and reality that conflicts with evolution. For those working in cancer research, evolution for these believers is necessary for their oncology work.


TE/EC does accommodate science in its most pure form but it does have other serious problems in my opinion. The theists who accept it and even medically work with it (Swamidass and Finlay) however evidently don't have a conflict with their theism and evolution. I write about possible serious problems with TE/EC here in the second half of that blog entry. Perhaps you may agree.


The main issue here in my opinion is that evolution appears to be naturalistic and materialistic. There appears to be no goals or planning. Natural selection sacrifices incredible numbers of offspring to get just a few replacement individuals into the next generation. Mutations to produce new genes are random. There have been 5 huge mass extinctions and over 99.9% of all species that have existed have gone extinct, some by rocks from space. Truthfully, what major creationist organizations attack is the apparent conclusion of many people looking at evolution, macroevolution, that it is all naturalistic and materialistic. No room for God. In addition, a close look at biology without cherry picking reveals no intelligent design.


13. What about love? Claim: Science can't explain love

Response: Not only can science explain and study it, but also marvel in the joy of it and not diminish it. "Understanding how chocolate tastes good doesn't diminish how good it tastes."



14. Incomplete Linkage Sorting (ILS)

It turns out that when comparing genomes there are many exceptions to the clustering of random DNA changes from ERVs, segmental duplications, DNA repairs, transposon elements (TEs) and pseudogenes. Normally thousands of these random DNA changes fit nicely into predicted phylogenetic evolutionary trees. As an example, TEs have been found to be inserted into gorillas and humans but not chimps. Doesn’t this invalidate using these markers for evolution? Not at all.

What is going on is called incomplete linkage sorting (ILS). Our genomes are made up of many different alleles, which are possible genes at a given location or locus. As an example, with the major blood group ABO, one can be OO, AO, BO, AB, AA or BB. Because we normally get one chromosome from each parent there are only two possible places for these specific multiple alleles. With the immune system for example there is an MHC complex where hundreds of possible alleles for a gene are available. Genes that have multiple possible alleles are called polymorphic. If speciation occurs rapidly relative to the time required for it to become fixed in a population (where all members have it), a new species may randomly lose particular genes just by chance and genetic drift when it splits off from the ancestor species.

Anti-evolutionists made a big deal in 2012 after the gorilla genome was sequenced and it was found that up to 30% of the chimp, human and gorilla genomes showed incomplete linkage sorting (5). Considering that a particular critic of evolution is perhaps the leading creationist geneticist the attempt at obscuration and misrepresenting the findings was breathtaking. We’ve met Dr. Tomkins before in several other blogs on this site. See human chromosome 2 fusion , pseudogenes, and especially comments by Dr. Zach Hancock. Dr. Tomkins is arguably the most prolific Young Earth Creationist writer in terms of genetics. It seems lost on anti-evolutionists that ILS is expected, noted and actually was predicted from population genetics by Kingman in 1982 (*). Instead of bad news for evolution this apparent anomaly in phylogenetic analysis actually supports evolution due to calculations, and the real apparent problem is why a top creationist apologist in genetics seems to have left his PhD back at his granting institution. For an explanation of ISL - it’s not easy to understand - see an article at The Panda’s Thumb and Freethought Blogs (7). One of the best insights possible into erroneous anti-evolution claims is drilling down on their arguments to expose fallacies, often committed by omission. * - see also discussion here: Understanding Incomplete Linkage Sorting. https://www.reddit.com/r/evolution/comments/2w42at/understanding_incomplete_lineage_sorting/#


15. A Stegosaurus carving? Young Earth Creationist claim.

"Atheists say that Christian's are the ones who deny evidence. But time and time again, atheists will deny this excellent and absolutely solid piece of evidence against their dogmatic religion of atheism. They have to have millions of years because without it, their worldview will collapse. They don't want the Bible to be true, so they go with humans and dinosaurs being separate by millions of years.

However, we have this archeological discovery where ancient people carved a Stegosaurus. Don't tell me how the anatomy is wrong, because what if it's just the artist's interpretation?" FB: Evolution and Creationism Open Debate. 11/29/2023


"This time it’s the silly “Stegosaurus at Ta Prohm” rumor. This myth has been popularized by young earth creationists*, who’ve argued that one particular small carving on a doorway at Ta Prohm depicts a Stegosaurus. Never mind that the entire temple is covered with carvings of fantastic and mythical creatures, this one carving is evidence that humans and dinosaurs co-existed. The carving is found within a series of other carvings depicting non-mythological creatures, such as monkeys, deer, birds, and water buffalo, and other scenes... So, what we would have in this doorway is a series of carvings of wild animals (with the exception of a domesticated water buffalo) that are frequently found in the forests of Cambodia. Maybe it’s a lizard, or a rhino, or a pangolin. But it is not a dinosaur." https://alisonincambodia.wordpress.com/2014/10/14/that-is-not-a-stegosaurus/?fbclid=IwAR3PvW-XKJl4S-0oxcJYI7j92gqiqkGjreiLDSfGxmwTHwQHtxcEgZQnZW0


More like the local rhinos with added decorations. This confirmation bias and motivated reasoning overload is common among YECs.




16. "Polystrate" Trees

To the anti-evolutionist, this is a "gotcha" for evolution. Fossil trees that supposedly span millions of years, thus completely disproving evolution in their view. Note that this is an argument put forward mainly by Young Earth Creationists. A simple Google of "polystrate" trees will show how popular these are in YEC circles, and YouTubes will demonstrate how gleeful they are that these findings supposedly are perfectly explained by a global flood and supposedly disprove evolution.



Ancient in situ lycopsid, probably Sigillaria, with attached stigmarian roots. Specimen is from the Joggins Formation (Pennsylvanian), Cumberland Basin, Nova Scotia. From: Michael C. Rygel via Wikimedia Commons



These fossil upright trees have been found in several places around the world. The term polystrate is not a recognized term in geology; it's a term coined by Young Earth Creationists. They explain them as a product of a global catastrophic Flood that occurred about 4,000 years ago.


What is the truth about them, and more importantly how do we know? What are the creationist PhDs not telling us? Lying by omission is still lying. These are actually formed by rare and infrequent localized flooding. The fact that they only occur in certain areas is a clue to what really happened. An 11 minute video by Erika details the main points that disprove this creationist claim. Below is her summary. 1. Polystrate is not an accepted geological term because they don't span millions of years of strata 2. The fossils show root growth after partial burial. Impossible for the creationist explanation in seawater but perfectly understandable by geology 3. Some of the upright fossil trees show regenerative growth - they were growing after their partial repeated burials as the trees tried to recover 4. We can see this type of repeated local flooding and partial burial of trees today in certain areas. The areas in the fossils and today show repeated sedimentary flooding partially burying the trees. The trees respond by growth until the next flooding and that continues through cycles.

5. Thus, when examining ALL the applicable evidence, these upright tree fossils actually disprove young earth creationism and are wonderfully explained by evolution and geology. Please watch this 11 minute video because she SHOWS the evidence that fits evolution and actually disproves them supporting a global flood. And she's entertaining! Perhaps the best 11 minutes you could spend today.




17. Human and chimp genomic similarities How similar are chimp and human genomes? Well, it depends on what one is comparing. Recall that we have 25,000 genes. The protein coding genes make up 20,000 and there are another 5,000 genes that code for RNA products that have functions with regulation for example but do not directly produce protein products. Enzymes that control just about everything are the main proteins produced. These genes that don’t produce proteins are called “non-coding”. Our genome contains about 3 billion pairs of ATCG letters but only a few million of those compose genes. For example, when a gene sequence is read to make a messenger RNA, many areas of the initial mRNA sections are cut out and thrown away and the active parts of the mRNA are then fused together for the final instructions to go to the protein ribosomal “factories”. The initial mRNA needs to be processed and refined before being sent to the ribosomes. The active areas in the mRNA are called exons and the sections that are nearly always thrown away and degraded are called introns. About 30% of our genome is made up of these introns which are a type of junk DNA. 


So, what we include in our chimp - human comparison matters. Do we just include the active genes which tend to be conserved in evolution (little changed over time and between species) or do we include introns or even parts of the chromosomes that have been inserted and deleted, called indels


It turns out that if we compare those 20,000 protein coding genes between humans and chimps the ATCG exact base sequences are 99% identical to every letter between us and chimps. If we include all the insertions and deletions, changes in the genome due to movements of genetic material, we are still 96% exactly the same as chimpanzees (1, 2). What then makes us different from chimps? We think it’s largely how and when those genes are turned on and off. And those regulatory genes are in the other parts of the genome. In other words, if you want to make a bigger more complex brain, you keep those genes active in embryological and fetal development turned on longer. That is an oversimplification but that is the general idea of how we can have 99% the same exact protein coding genes and yet have important phenotypic differences between humans and chimps.



Anti-evolutionist attacks on the percentages


Since these similarities are best explained by evolution and evolution deniers presuppose and assert that humans were created separately from all the other great apes, there has been a concerted effort to lower the observed DNA similarity percentages between us and chimps/bonobos.


For example, Tomkins in 2013 wrote an article claiming that the real similarity between chimps and humans was only 70%; all the other scientists except his small fringe group that thinks the universe is only about 6,000 years old are purposely misleading with the findings (3). Notice that Tomkins did not publish in an established peer reviewed scientific journal where his assumptions could be evaluated. Novella showed in 2015 that Tomkins’ attempt was not credible:


"So how does Tomkins come up with 70%. Well, he is not comparing point mutations of aligned segments. He is comparing chromosomes to see how many segments line up to some arbitrary amount. As many others have already pointed out, this result is not wrong, it’s just irrelevant. Well, it might also be wrong. Others have found it difficult to reproduce his results. But even if his analysis is accurate, it is simply the wrong analysis to apply to dating the last common ancestor.  To explain the problem further, he is applying mutation rates for point mutations (changing a single base pair) to other types of mutations, like gene duplications or insertions, that might change thousands or millions of base pairs with a single mutation. He is essentially treating a single mutation that results in the insertion of 10,000 base pairs into the genome as if it were 10,000 separate mutations of single base pairs.” (4)


Another creationist article cited Luskin in an attempt to throw doubts on the figures scientists have produced and confirmed. They also attempt to mock scientific findings that show common descent and human evolution (5). Humans and chimps are 99% or 96% exactly the same depending on which parts of the genome are compared. These figures are sound, confirmed and most consistent with evolution. 



Literature Cited.








18. What about Edward Blyth? "One of the tactics that creationists use to cast doubt on evolution is to suggest that Darwin undeservedly received the credit for the theory of natural selection and misappropriated the idea from the work of other scientists (see for example http://www.uncommondescent.com/intelligent-design/was-blyth-the-true-scientist-and-darwin-merely-a-plagiarist-and-charlatan/). This claim is as false as the “science” of creationism itself.As any student of science and history knows, new discoveries in science seldom emerge from a single source. Many of the advancements of science occur when new knowledge, derived from a variety of sources, is blended together to form new theories. Credit for scientific discovery is often a messy business and this was certainly the case with Darwin.

Contrary to Looy’s claim, natural selection was first described not by Blyth (or Darwin for that matter), but by the ancient Greek philosophers Empedocles and Aristotle in the third and fourth centuries BCE. Many scientists and philosophers in the centuries that followed contributed to the understanding of the adaptation of species due to environmental and competition pressures: al-Jahith, Harvey, Paley, Linnaeus, Buffon, Mathus, Lamarck, and Darwin’s grandfather, Erasmus Darwin, to name a few (see http://evolution.berkeley.edu/evolibrary/article/0_0_0/history_index_01). Blyth contributed to the pool of knowledge with his insightful observations of bird species (specifically the birds of India) and his analysis of selective breeding practices of domesticated animals in a series of articles in The Magazine of Natural History from 1835 to 1837." https://ncse.ngo/edward-blyth-creationist-or-just-another-misinterpreted-scientist

Even the biologist and creationist Dr. Todd Wood notes in his article that Darwin did not plagiarize natural selection. There is no Darwin Conspiracy: https://answersresearchjournal.org/no-darwin-conspiracy/



19. Is Earth really at the Center of the Universe?

Claim: Cosmological observations (Cosmic Background Radiation, for example) indicates we are at the center of the universe. This confirms a Biblical worldview of Genesis 1:1


Response: First, yes it does appear that way. But it’s an illusion because anywhere in the universe will look to an observer that they are the center of the universe. Most creationists who think they have a Genesis gotcha appeal to two sources. The most common referenced quote is from Lawrence Krauss in 2006:“That is, we live in one universe, so we're a sample of one. With a sample of one, you have what is called a large sample variance. And maybe this just means we're lucky, that we just happen to live in a universe where the number's smaller than you'd predict. But when you look at CMB map, you also see that the structure that is observed, is in fact, in a weird way, correlated with the plane of the earth around the sun. Is this Copernicus coming back to haunt us? That's crazy. We're looking out at the whole universe. There's no way there should be a correlation of structure with our motion of the earth around the sun — the plane of the earth around the sun — the ecliptic. That would say we are truly the center of the universe.


The new results are either telling us that all of science is wrong and we're the center of the universe, or maybe the data is imply incorrect, or maybe it's telling us there's something weird about the microwave background results and that maybe, maybe there's something wrong with our theories on the larger scales. And of course as a theorist I'm certainly hoping it's the latter, because I want theory to be wrong, not right, because if it's wrong there's still work left for the rest of us.” The Energy of Empty Space That is Not Zero


Another quote often put forward is from Hubble in his 1937 book:“…Such a condition would imply that we occupy a unique position in the universe, analogous, in a sense, to the ancient conception of a central Earth.…This hypothesis cannot be disproved, but it is unwelcome and would only be accepted as a last resort in order to save the phenomena. Therefore we disregard this possibility…the unwelcome position Here of a favored location must be avoided at all costs… such a favored position is intolerable…. Therefore, in order to restore homogeneity, and to escape the horror of a unique position…must be compensated by spatial curvature. There seems to be no other escape.”

No, we are not the center of the universe. There are many sources that will clarify that the creationist is not understanding what the science is nor what the context of their quotes are. A quick Google search will turn up many:

This does not mean, however, that we are at the centre of the Universe; it just means that we are at the centre of our observable Universe. A fundamental principle in our understanding of the Universe itself, called the Cosmological Principle, states that the Universe is homogeneous and isotropic on the largest scales. That means that on the whole, the Universe as seen from any vantage point (even one that is 15 billion light-years away from us!) will measure a spherical observable Universe with a radius of 15 billion light-years.” https://www.reddit.com/r/DebateAnAtheist/comments/z8ukqg/the_earth_appears_to_be_the_center_of_the_universe/

And:“In summary, the data received by WMAP and Planck shows that we are the center of the universe. However, there is no evidence to suggest that we are literally at the center of the universe. Multiple other stellar systems and galaxies are seen to be aligned around us, but there is no apparent pattern that suggests we are at the center.”“We are the exact center of the OBSERVABLE universe. That's purely because we observe things with light, we can see in all directions at most 13.6 billion years because time started then and light didn't exist before it. So we exist in one location, what does one location extruded in all directions the same distance produce? A perfect sphere with the original point at the center. It makes no difference what's beyond that, you are by definition the center of the observable universe because observation in local.”


Krauss has also made comments about how his quotes have been taken out of context and used in a film promoting of all things - geocentrism!:

https://slate.com/technology/2014/04/lawrence-krauss-on-ending-up-in-the-geocentrism-documentary-the-principle.html To summarize to the first point the creationists are quoting these scientists out of context. Of course they don’t believe there is any evidence that we are at the center of the universe. Just like it appears that the earth is flat, immobile and the sun is rotating around us is not true. It only appears that way. This link also has a good short discussion of how to property interpret the CMB findings instead of projecting a religious presupposition onto the data:



No, Genesis 1:1 does not say the universe was created from nothing

Now to the second point. The Hebrew interpretation of Genesis 1:1 has been most commonly translated: “In the beginning God created the heavens and the earth”. This would indicate an ex nihilo creation from nothing at a single point in time. But Hebrew scholars the past decades have noted that Gen 1:1 can’t be taken by itself but must be understood in the context of all three first verses, and if properly interpreted Genesis is not talking about creation out of nothing.


“First, as many modern Hebraists have noted, Genesis 1:1 opens with a temporal clause. The precise meaning of its first word, bere’shît, is literally “in the beginning of.” This is a complex grammatical topic, but simplified, the way in which the first word has come to be vocalized, indeed the first letter, bet, implies that grammatically the word is in the construct state, that is a noun which is followed by another noun. A literal translation is “in the beginning of.” And this is exactly what we find as the proper understanding of bere’shît when this same word appears elsewhere in the Hebrew Bible. So, for example, the Hebrew of Jeremiah 27:1, bere’shît mamelekhet yihôyaqim, is properly rendered: “In the beginning of the kingdom of Jehoiakim.” But the grammatical problem in Genesis 1:1 is that bere’shît is not followed by a noun but rather a verb-subject pair: bere’shît bara’ ’elohîm. Thus a literal rendering of the first three words of Genesis 1:1 is impossible: “In the beginning of God created.” Thus many modern translations have sought to capture the temporal aspect in the opening word of the book of Genesis by rendering the Hebrew: “In the beginning of God’s creating…” or “In the beginning when God created…” or even “When God began to create…” “Despite strong traditional and often authoritative interpretative claims that were formed centuries after this ancient text was written and devoid of knowledge about its historical and literary context, the opening of Genesis 1 does not depict a creatio ex nihilo, that is a creation out of nothing. The Hebrew text is clear on this point… Rather, what the text of Genesis 1:2 informs us is that when God began to create, earth in some manner of speaking already existed as a desolate, formless, empty waste—tohû wabohû in Hebrew, literally “desolation and waste”—in the midst of a dark surging watery abyss (tehôm).


A Hebrew Scholar in this 10 min demonstrates the best interpretation:



21. No, Atheism is not a religion


First, what is atheism? The word gives us an important clue. The prefix “a” in English means “not or without”. Properly defined by scholars of atheism and the word itself, atheism is simply the lack of belief in God due to a lack of evidence. It is not a positive assertion that there are no Gods anymore than bald is a hair color. There are no creeds, no systematic practices that all atheists share, no atheist bible or sacred book, no centralized beliefs. A lack of belief can’t be a belief. This is discussed more here: Atheism. 


Secondly, what do we mean most of the time by religion? One can apply a literary device of the term that may be clever but loses it’s main meaning, such as saying golf or football are someone’s “religion”. But that’s not how people view what it means to be religious most of the time. 


Some definitions of religion include:


“the belief in and worship of a superhuman power or powers, especially a God or gods.

ideas about the relationship between science and religion”. ~ Oxford Dictionary

“a personal set or institutionalized system of religious attitudes, beliefs, and practices” “the service and worship of God or the supernatural” “commitment or devotion to religious faith or observance” ~ Merriam-Webster "By religion, then, I understand a propitiation or conciliation of powers superior to man which are believed to direct and control the course of nature and of human life"   ~ James George Frazer, (The Golden Bough).

"[Religion is] the belief in Spiritual Beings" (Edward B Tylor, Primitive Culture)


Atheism does not fit any of the common definitions for a religion that involves the supernatural and the practices of a religion. 


Third, religion forms the foundation of many worldviews. One way to know atheism is neither a religion nor a worldview is to note how easy it is to find atheists with totally opposite worldviews. For example the atheists Stalin and Pol Pot killed and murdered for the ideology of communism and yet there are many atheists that are kind and compassionate, even some that have founded charities to help those struggling in life. They killed in the name of communism not atheism. See # 11, the blog page you are on currently. Worldviews are a way of living one’s life, deriving purpose, meaning and ethics. More is discussed here: Worldviews 


Therefore, atheism can’t be a religion. It does not fit the most common definitions of a religion. There is no central creed or beliefs that atheists practice. There is no belief in the supernatural. Lastly, different atheists follow different ethics and behaviors; there is no foundational or central assertions, just the lack of belief in a deity due to a lack of convincing evidence for the theistic claim. 



22. No, Evolution is not a Religion


First, what do we mean most of the time by religion?  One can apply a literary device of the term that may be clever but loses it’s main meaning, such as saying golf or football are someone’s “religion”. But that is not how people view what it means to be religious most of the time. 


Some definitions of religion include: “the belief in and worship of a superhuman power or powers, especially a God or gods.

"ideas about the relationship between science and religion”. ~ Oxford Dictionary

“a personal set or institutionalized system of religious attitudes, beliefs, and practices” “the service and worship of God or the supernatural” “commitment or devotion to religious faith or observance” ~ Merriam-Webster "By religion, then, I understand a propitiation or conciliation of powers superior to man which are believed to direct and control the course of nature and of human life"   ~ James George Frazer, (The Golden Bough).

"[Religion is] the belief in Spiritual Beings" (Edward B Tylor, Primitive Culture)


Secondly, what do scientists mean when they use the term evolution, especially since the 1940s?  It is the change in allele (gene) frequencies in a population through generations. As mutations occur and natural selection and other mechanisms filter out some genes over others, in successive populations the proportion of certain genes in successive populations will change. This is discussed in more detail  here: evolution . We thus see evolution every day - in the field, the lab, and even in the hospital through for example antibiotic resistance in bacterial populations.


Third and perhaps most important because it falsifies this claim that evolution can be a religion is the fact that evolution is accepted by thousands of scientists who do have different religious views. There are Christian, Muslim, Hindu, agnostic, and atheist scientists who accept evolution due to the overwhelming evidence for it. Most have mutually exclusive religious beliefs or they lack belief.


Lastly, religion forms the foundation of many worldviews. One way to know evolution is neither a religion nor a worldview is to note how easy it is to find scientists with totally opposed worldviews who share an affirmation that evolution is true. From the Pope to Richard Dawkins. To the evangelical debater and philosopher William Lane Craig to the late Christopher Hitchens, or Sam Harris. For example the atheists Stalin and Pol Pot killed and murdered for the ideology of communism (see more # 11 this blog page) and yet there are many atheists that are kind and compassionate, even some that have founded charities to help those struggling in life. A worldview is a set of principles and a way of living one’s life. More is discussed here: Worldviews


Evolution is just the finding of how, from where, what and when species arise on our planet. It can’t be a religion because it is the study of the natural, not the supernatural and people who do have mutually exclusive religious beliefs can agree,. accept, and work together with this grand scientific theory. 



23. Shapiro, Noble Show That Darwinism Is In Deep Trouble? Claim: Many secular biologists are showing that Darwinian evolution is in trouble. There was a meeting and symposium in England even that was held to detail many of the problems and inadequacies. Response: No, Neo-Darwinism is alive and well. First, note that Shapiro, Noble and few others are supporters of evolution fully. They don't think the mechanism of Dawin is sufficient. Please understand that the Theory of Evolution is not Darwinism. Darwin proposed a mechanism for evolution per his book title: "On The Origin of Species by Natural Selection..." Are there other mechanisms? Sure, such as Lateral Gene Transfer, Endosymbiosis, Genetic Drift and Nearly Neutral Theory especially important at the DNA level. Natural Selection is alive and well and stronger than ever but even IF it was discarded we'd still have all the overwhelming evidence for evolution. Evolution is a fact (see above number 10). Now what is telling is despite these Third Way scientists', as they call themselves, books and publications no scientists besides themselves, creationists and Intelligent Design believers take them seriously.


For those who think the scientists of the Third Way are onto something special about evolutionary theory, to be fair they must read critical specific reviews about their assertions from well respected evolutionary biologists and biochemists also.


A. Denis Noble: The illusions of Denis Noble


B. James Shapiro

The illusions of James Shapiro



  • The Modern Synthesis (MS) was not based on a "gene-centric" view.

  • For the past 50 years, no respectable scientist, and no knowledgeable expert in molecular evolution, has restricted the definition of "gene" to just protein-coding genes.

  • For the past 50 years, no expert in molecular evolution has ever thought that the genome is just a collection of protein-coding genes.

  • For the past 50 years, experts in molecular biology have known about transposons and have considered the view that some of them might be "controlling elements." They have concluded that most transposon-related sequences are just fragments of defective transposons with no biological function.

  • Nobody cares whether mobile genetic elements fit within the narrow confines of the Modern Synthesis as described by Huxley and other in the 1940s because no expert in molecular evolution has believed in that view of evolution since the late 1960s.

  • The Britten and Kohne paper established that the genomes of most multicellular eukaryotes contain large amounts of repetitive DNA. This was an attempt to resolve the C-value paradox. Britten and Kohne didn't like the idea that this could be junk DNA so they offered some speculation about function. However, further data established that most of this repetitive DNA is, indeed, junk and Britten and Kohn's speculations have been discredited. Britten and Kohn were attempting to interpret their result within the context of the adaptationist views that characterized the the Modern Synthesis back then. The correct interpretation of their results came with the overthrow of the Modern Synthesis and the adoption of a new view of evolutionary theory that focused on Neutral Theory, Nearly-Neural Theory, and the importance of random genetic drift. Shapiro and Noble missed that revolution so they continue to attack an old-fashioned strawman version of evolutionary theory."

To be continued, most likely as I become familiar with further popular anti-evolutionist arguments.





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