Are We Really 98% Chimp?

[The Barbarian]

36 minutes ago, Retrobyter said:

Shalom, @Ogner.

We also need to understand that DNA is not just a chain, but it is also THREE-DIMENSIONAL, and they're in the process of discovering that it is even FOURTH-DIMENSIONAL.  It wraps upon itself so that portions of the double-helix are overlapped with other portions to perform certain tasks. And, that overlap CHANGES with the age of the individual! In this way, DNA is NOT static, but DYNAMIC as it ages.

Right:

BioScience, Volume 54, Issue 11, November 2004

The Genomic Palimpsest: Genomics in Evolution and Ecology

Abstract

Genomics is the discipline that has grown up around the sequencing and analysis of complete genomes. It has typically emphasized questions that involve the biological function of individual organisms, and has been somewhat isolated from the fields of evolutionary biology and ecology. However, genomic approaches also provide powerful tools for studying populations, interactions among organisms, and evolutionary history. Because of the large number of microbial genomes available, the first widespread use of genomic methods in evolution and ecology was in the study of bacteria and archaea, but similar approaches are being applied to eukaryotes. Genomic approaches have revolutionized the study of in situ microbial populations and facilitated the reconstruction of early events in the evolution of photosynthetic eukaryotes. Fields that have been largely unaffected by genomics will feel its influence in the near future, and greater interaction will benefit all of these historically distinct fields of study.

[Ogner]

43 minutes ago, The Barbarian said:

So far, everything we've learned about it, further confirms our common ancestry.

Well, you probably haven't read much in the genetics literature...

Emergent Properties of Gene Regulatory Networks: Models and Data

https://link.springer.com/chapter/10.1007/978-94-007-6803-1_3

If you think that's what genetics tells us about evolution, I can tell that you know almost nothing about genetics.    Read some of the links I left you, and learn a little about it.    Your assumptions about genomes are a "fundamental distortion of reality."

 

you claim that I know nothing about genetics and that my Shakespeare book analogy distorts reality, but let me explain why that’s not the case. I’ve carefully reviewed the article "Emergent Properties of Gene Regulatory Networks: Models and Data" you referenced, and it doesn’t contradict my position—it actually supports the idea that simply comparing DNA by percentage similarity is an oversimplification.

My book analogy highlights that the often-cited 98% DNA similarity between humans and chimps doesn’t capture the full complexity. I base this on evidence showing that, when accounting for all DNA differences—substitutions, insertions, deletions, rearrangements, and so-called "junk" DNA—the divergence is actually 13–19%, or 400–600 million nucleotides out of 3.2 billion. This makes the idea of evolution through random mutations over 6 million years mathematically implausible, as accumulating such a number of changes would require an unrealistic mutation rate. I believe DNA is not a product of random evolution but of intentional design, where similarities and differences between species are purposefully created.

The article you cited discusses gene regulatory networks (GRNs) and their emergent properties, showing how they drive complex biological behaviors like cell differentiation. It confirms that even small DNA changes, amplified by stochastic effects, can lead to significant phenotypic differences. This aligns with my analogy: if DNA is a book, the 98% similarity is just the "syntax," while the "semantics" (regulatory logic via GRNs) and "narrative" (phenotypic functions) define the real differences. However, this doesn’t prove evolution. On the contrary, the complexity of GRNs and their ability to create diversity from small changes can be interpreted as part of a designed system, where each "book" (genome) is crafted for a unique purpose.

You argue that genetics confirms evolution, but I disagree. My book analogy doesn’t distort reality—it emphasizes that DNA is too complex to be the result of random mutations and that percentage similarity doesn’t explain why humans and chimps are so different. I don’t deny the scientific data on GRNs, but I interpret them differently: DNA isn’t a text that "evolved" but a designed system where every detail matters.
 

Edited March 26 by Ogner

[Ogner]

1 hour ago, Retrobyter said:

Shalom, @Ogner.

We also need to understand that DNA is not just a chain, but it is also THREE-DIMENSIONAL, and they're in the process of discovering that it is even FOURTH-DIMENSIONAL.  It wraps upon itself so that portions of the double-helix are overlapped with other portions to perform certain tasks. And, that overlap CHANGES with the age of the individual! In this way, DNA is NOT static, but DYNAMIC as it ages.

 Shalom,  Retrobyter, I completely agree with you that DNA isn’t just a linear chain but a complex three-dimensional, and even dynamic, system that changes over time. You’re absolutely right to point out that DNA folds upon itself, creating overlaps that shift with age, making it dynamic rather than static. I understand your mention of a "fourth dimension" to likely refer to the temporal changes in DNA’s structure and function, such as epigenetic modifications or chromatin remodeling, which affect gene expression throughout an individual’s life.
This complexity of DNA supports the perspective I expressed in my Shakespeare book analogy. I argued that comparing human and chimp DNA solely by sequence (e.g., the 98% similarity claim) is like comparing two books by their page count, ignoring their content. But as you’ve noted, DNA isn’t just a text—it’s a multi-layered system where three-dimensional organization and dynamics play a critical role. Moreover, when we account for all DNA differences—substitutions, insertions, deletions, rearrangements, and "junk" DNA—the divergence between humans and chimps is actually 13–19%, or 400–600 million nucleotides. Random mutations over 6 million years couldn’t account for such changes—it’s mathematically impossible.
I believe this incredible complexity of DNA, including its three-dimensional and dynamic nature, points to it being a product of intentional design, not random evolution. If DNA is a book, it’s a book written with extraordinary precision, where every loop, every overlap, and every age-related change is designed to fulfill specific functions. Your insight about DNA’s dynamics only strengthens my conviction that evolutionary theory cannot explain such complexity, and we should view DNA as the result of intelligent design.

[timf]

If one considers that the genetic code is the blueprint for the body, one would expect similarities for respiratory system, neurology, musculature, and things like the metabolization of carbohydrates and the disassembly and fabrication of proteins.

I am not sure I would agree with the 2% number as it implies a level of accuracy that I think exceeds actual understanding. Even less well understood are epigenetics and their influence.

However, I would not disagree with a statement like, Genetically we are closer to an ape than to a daffodil.

Perhaps a focus on the physical distracts from things like the soul and spirit.

The complexity and beauty of the machinery of life point undeniably to the hand of the creator.What amazes me is that so many of those whose career is studying this machinery, deny the one that created it.

 

[The Barbarian]

50 minutes ago, Ogner said:

you claim that I know nothing about genetics and that my Shakespeare book analogy distorts reality, but let me explain why that’s not the case. I’ve carefully reviewed the article "Emergent Properties of Gene Regulatory Networks: Models and Data" you referenced, and it doesn’t contradict my position—it actually supports the idea that simply comparing DNA by percentage similarity is an oversimplification.

You were under some misconceptions about what genetic similarly means and what we know about animal genomes.   And I already showed you that simple percentages are not as significant as the details of genes between closely related species like humans and chimpanzees.   Would you like me to show you some more examples?

52 minutes ago, Ogner said:

I base this on evidence showing that, when accounting for all DNA differences—substitutions, insertions, deletions, rearrangements, and so-called "junk" DNA—the divergence is actually 13–19%, or 400–600 million nucleotides out of 3.2 billion.

If you thought about it, you might realize why the divergence in non-coding DNA between closely-related species should be greater than that between coding genes.   Do you see why?   The difference you cite is another confirmation of Darwinian theory.

50 minutes ago, Ogner said:

argued that comparing human and chimp DNA solely by sequence (e.g., the 98% similarity claim) is like comparing two books by their page count, ignoring their content.

No.   It would be like comparing two books by the sequences of words in the text.   Which would still be less accurate than looking at the genes themselves.

52 minutes ago, Ogner said:

Moreover, when we account for all DNA differences—substitutions, insertions, deletions, rearrangements, and "junk" DNA—the divergence between humans and chimps is actually 13–19%, or 400–600 million nucleotides. Random mutations over 6 million years couldn’t account for such changes—it’s mathematically impossible.

Perhaps we can test that.   Most of us have about 60 mutations found in neither of our parents.    

https://www.livescience.com/33347-mutants-average-human-60-genetic-mutations.html

So let's suppose a population of 100,000 individuals.   That would be about 6,000,000 mutations per generation.    Let's say a generation time of 25 years.    Over 3,000,000 years, (approx time since diversion of chimps and humans) then 120,000 generations.   So about 720 billion mutations, about 1200 times the needed number to match today.   Of course natural selection would trim out any that turned out to be actually harmful.    Most,as you probably know, don't affect survival measurably.   Your math is at fault now.   And of course, Darwin's great discovery was that evolution isn't merely 

random.   

1 hour ago, Ogner said:

If DNA is a book, it’s a book written with extraordinary precision, where every loop, every overlap, and every age-related change is designed to fulfill specific functions.

You have way too much confidence in it.   There are lots of things like the GULO gene, that just don't do much of anything.   But over 120,000 generations of natural selection, it's not hard to see why genomes work pretty well in spite of everything.

1 hour ago, Ogner said:

Your insight about DNA’s dynamics only strengthens my conviction that evolutionary theory cannot explain such complexity, and we should view DNA as the result of intelligent design.

See above.   And even most IDers now admit that the "design" was in creating a universe in which such things develop by natural processes.    Read Michael Denton's Nature's Destiny to learn why.

[The Barbarian]

1 hour ago, timf said:

If one considers that the genetic code is the blueprint for the body, one would expect similarities for respiratory system, neurology, musculature, and things like the metabolization of carbohydrates and the disassembly and fabrication of proteins.

In the case of humans and chimps, almost everything already existed long before humans and chimps diverged.    The Krebs Cycle. for example,  is remarkably constant for all living things on Earth.   

Evolutionary lineages are indicated by homologies, not analogies.     Hence humerus, ulna, radius etc. for mammals showing common descent, rather than wings legs or fins, which exist in various analogous forms.   Think whales, bats, horses, humans for homology, and bats, birds, dragonflies, and flying fish for analogy.    Homology indicates common descent; analogy does not.

Edited March 26 by The Barbarian

[The Barbarian]

1 hour ago, Ogner said:

You argue that genetics confirms evolution, but I disagree.

Doesn't matter.   For example, humans and other apes have different numbers of chromosomes.    But one human chromosome matches precisely with two chromosomes found on other apes, right down to the remains of telomers precisely where the fusion occurred.   I mentioned the vitamin C gene in all apes which is broken, but most similarly broken among apes with all other mammals in an outgroup.

And of course, we can check the idea that genetic similarity indicates common descent by testing it on organisms of known descent.   Always works.

One highly-conserved molecule in all living things is cytochrome C.   Nevertheless, there are small differences in the molecule among living things which occurred by mutation in parts of the molecule that did not adversely affect its activity.   Not surprisingly, the phylogeny obtained by the number of amino acid differences nicely matches evolutionary phylogenies obtained by other evidence.

Turns out, genetics confirms Darwin's predictions very well.

 

[Ogner]

10 hours ago, The Barbarian said:

No.   It would be like comparing two books by the sequences of words in the text.   Which would still be less accurate than looking at the genes themselves.

 I believe my analogy holds, and here’s why: even a small difference of 13–19% in DNA can radically change its "meaning," just as a tiny change in a book can completely alter its story—sometimes even flipping the meaning to the opposite.
For example, consider the question: How do you think Pilate’s wife asked for Barabbas or Jesus? In the original Greek text, a single particle can change the entire meaning of the passage. Another example: What were the Jewish leaders, high priests, and elders envious of? The single word "envy" in the text creates so much confusion showing how one word can shift the understanding of an entire narrative.

Now, in our analogy, we’re talking about a 13–19% difference between human and chimp DNA. At first glance, 13–19% might seem small, but it’s actually a massive gap—it’s not just one or two words. It’s 400–600 million nucleotides, and in our book analogy, those nucleotides are like letters. This isn’t a single word, a single page, or even a single chapter. It’s not even one book, like a Gospel within the Bible. Let’s break it down with the Bible as an example, using the King James Version (KJV) for consistency:
The Gospel of Matthew: about 97,000 letters.

The Gospel of Mark: about 58,000 letters.

The Gospel of Luke: about 104,000 letters.

The Gospel of John: about 78,000 letters.

Adding them up: 97,000 + 58,000 + 104,000 + 78,000 = 337,000 letters. The entire Bible (KJV) has approximately 3,566,480 letters. So, the four Gospels make up (337,000 ÷ 3,566,480) × 100 ≈ 9.4% of the Bible. By a similar calculation, the entire New Testament accounts for about 22.3% of the Bible. That means a 13–19% difference in DNA is equivalent to 9.4–22.3% of the Bible’s text.
Now, imagine removing 9.4–22.3% of the Bible—say, all four Gospels or even the entire New Testament. The unified story and meaning of the Bible would be completely lost. Yet, with the Bible, we know the language it’s written in. We can read and understand not only the meaning of the words but also the overarching plot. Even then, there are still disagreements in interpreting the text and the Bible as a whole due to small nuances.
In the case of DNA, however, we don’t even know the language, the meaning of the "words," or the overall "plot." We’re still deciphering how DNA works—its "syntax" (the sequence of nucleotides) is known, but its "semantics" (how it’s regulated) and "narrative" (the biological functions it produces) remain largely unclear. So, counting the sequence of letters in DNA, without understanding the language, and then claiming humans are 98% chimp is misleading. On top of that, the comparison isn’t even fully accurate letter by letter—it’s not like the books match page for page. A 13–19% difference means entire sections, equivalent to whole books like the Gospels (9.4%), are different or missing, completely changing the "story" of the DNA.
That’s why my analogy stands: a 13–19% difference isn’t small—it’s a chasm that can fundamentally alter the meaning, just as a single word or particle can change the interpretation of a biblical text. 

The Bible needs to be understood, not just have its letters counted. Similarly, with DNA, we need to understand it, not just count its letters.  Can you imagine what biblical studies would look like if scholars could only count letters Bible?

 

[timf]

How would one differentiate between assuming that commonalities prove descent as opposed to commonalities proving a single designer?

[Ogner]

11 hours ago, The Barbarian said:

You were under some misconceptions about what genetic similarly means and what we know about animal genomes.   And I already showed you that simple percentages are not as significant as the details of genes between closely related species like humans and chimpanzees.   Would you like me to show you some more examples?

 I appreciate your offer to provide more examples, but I don’t think I’m under misconceptions about genetic similarity. My point is that focusing on simple percentages—like the 98% similarity claim—misses the bigger picture. The article you referenced, "Emergent Properties of Gene Regulatory Networks: Models and Data," shows that DNA is far more complex than just a sequence of letters, with regulatory networks creating significant differences even when sequences look similar. I’m not denying that genes between humans and chimps share similarities, but I’m questioning whether those similarities prove evolution.

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If you thought about it, you might realize why the divergence in non-coding DNA between closely-related species should be greater than that between coding genes. Do you see why? The difference you cite is another confirmation of Darwinian theory."

 I understand that you’re saying non-coding DNA (the parts that don’t directly make proteins) might change more than coding DNA because it’s less critical for survival, according to evolutionary theory. But I don’t see how this confirms Darwinian theory. A 13–19% divergence—400–600 million nucleotides—is a massive gap. If non-coding DNA changes so much, it only highlights how different humans and chimps are, even in parts that evolutionists often call "junk." I believe this level of difference points to a designed system, where every part of DNA, coding or not, has a purpose we don’t fully understand yet. The huge divergence doesn’t fit with the idea of gradual changes through evolution—it suggests a fundamental difference from the start.

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"Perhaps we can test that. Most of us have about 60 mutations found in neither of our parents. [Link to article] So let's suppose a population of 100,000 individuals. That would be about 6,000,000 mutations per generation. Let's say a generation time of 25 years. Over 3,000,000 years, (approx time since divergence of chimps and humans) then 120,000 generations. So about 720 billion mutations, about 1200 times the needed number to match today. Of course natural selection would trim out any that turned out to be actually harmful. Most, as you probably know, don't affect survival measurably. Your math is at fault now. And of course, Darwin's great discovery was that evolution isn't merely..."

I see your calculation, but I don’t think my math is at fault—it’s the assumptions behind your numbers that I question. You say 60 mutations per person per generation could add up to 720 billion mutations over 3 million years in a population of 100,000. But the 400–600 million nucleotide difference between humans and chimps isn’t just about random mutations piling up. Most mutations are neutral or harmful, as you noted, and natural selection would remove the harmful ones. However, for evolution to work, you need mutations that create new, functional traits—like the ones that supposedly turned a chimp-like ancestor into a human with speech, complex thought, and upright walking. The odds of random mutations creating such complex, coordinated changes in just 3 million years (not 6 million, as I previously stated, following your timeline) are incredibly low—some argue it’s mathematically impossible. I believe this level of difference and complexity points to a designed system, not random changes over time.

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You have way too much confidence in it. There are lots of things like the GULO gene, that just don’t do much of anything. But over 120,000 generations of natural selection, it’s not hard to see why genomes work pretty well in spite of everything."

I don’t think I have too much confidence in the precision of DNA—I think evolution underestimates its complexity. You mention the GULO gene, which in humans doesn’t work to produce vitamin C, unlike in some animals. Evolutionists call it a "broken" gene, but just because we don’t understand its function doesn’t mean it’s useless. Science often discovers purposes for so-called "junk" DNA years later. My analogy of DNA as a book written with extraordinary precision stands: every loop, overlap, and change might have a purpose we don’t yet see. Over 120,000 generations, natural selection might refine a system, but I don’t believe it can create the intricate design we see in DNA from scratch. The complexity of DNA suggests it was designed to work this way from the beginning, not that it evolved through trial and error.

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"See above. And even most IDers now admit that the 'design' was in creating a universe in which such things develop by natural processes. Read Michael Denton’s Nature’s Destiny to learn why."

I’ve noted your points above, but I don’t agree that the complexity of DNA’s dynamics can be explained by natural processes, even if some intelligent design proponents, as you say, believe the universe was set up to let things develop naturally. I haven’t read Michael Denton’s Nature’s Destiny, but I’ll look into it. However, my view remains that the intricate, three-dimensional, and dynamic nature of DNA—where even small changes can lead to vast differences—points to a purposeful design, not a universe left to evolve on its own. A 13–19% divergence between humans and chimps, combined with the complexity of how DNA functions, suggests to me that it was created with intention, not that it developed through random natural processes over time.