Design flaws in organisms indicate evolution, not intelligent design

[Compassionist]

The existence of design flaws in living organisms is often cited as evidence for evolution by natural selection rather than intelligent design by an all-loving, all-knowing, and all-powerful deity. If such a being existed and created life intentionally, we might expect optimal design — yet what we see instead are structures and processes that are inefficient, prone to failure, or even harmful.
Here are some significant biological design flaws that point to evolution rather than perfect design:
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1. Human Birth Canal vs. Big Brain
• Flaw: Human babies have large heads due to our large brains, but the human pelvis is narrow for bipedal walking.
• Result: Childbirth is extremely painful and dangerous — a leading cause of death historically.
• Evolutionary Explanation: Our ancestors evolved larger brains and upright walking separately, leading to a dangerous compromise.
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2. Wisdom Teeth
• Flaw: Most people don't have room for third molars, causing impaction, infections, and pain.
• Result: Many need surgery to remove them.
• Evolutionary Explanation: Our ancestors had larger jaws due to diet, but modern humans' jaws shrank faster than tooth evolution could keep up.
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3. Human Retina Is Backward
• Flaw: The photoreceptor cells in the human eye are behind layers of neurons and blood vessels.
• Result: Creates a blind spot and reduces image quality.
• Evolutionary Explanation: The eye evolved incrementally, not from a clean-slate design.
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4. Recurrent Laryngeal Nerve (Giraffe Example)
• Flaw: This nerve travels from the brain to the larynx, but loops around the aorta.
• Result: In giraffes, it travels over 15 feet instead of a direct path of a few inches.
• Evolutionary Explanation: It's a leftover from fish ancestors, where this path made sense. Evolution modified existing structures rather than redesigning from scratch.
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5. Human Menstrual Cycle
• Flaw: Humans shed the uterine lining even if not pregnant, wasting resources and causing pain.
• Result: Menstrual cramps, anemia, mood changes.
• Evolutionary Explanation: Other mammals reabsorb the lining. Our approach may have evolved due to pathogen risks in internal fertilization.
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6. Shared Path for Food and Air
• Flaw: The esophagus (food) and trachea (air) share an entrance.
• Result: Risk of choking — a leading accidental cause of death.
• Evolutionary Explanation: The throat evolved in stages, without foresight.
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7. Human Spine and Back Pain
• Flaw: Our spine is an S-curve not ideally suited for upright walking.
• Result: Many people suffer chronic back pain, herniated discs, etc.
• Evolutionary Explanation: Our ancestors were quadrupeds. The upright posture evolved later, leading to inefficient structure.
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8. Brain Vulnerability and Mental Illness
• Flaw: The brain is highly energy-consuming and prone to many dysfunctions.
• Result: High rates of depression, anxiety, bipolar disorder, schizophrenia, etc.
• Evolutionary Explanation: Natural selection favored reproductive success, not mental wellness or long-term wellbeing.
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9. Knee Joint Design
• Flaw: Knees bear immense strain, especially the ACL (anterior cruciate ligament), which often tears.
• Result: Common injuries in sports and aging.
• Evolutionary Explanation: Knees evolved from quadruped ancestors, not optimally engineered for bipedal running and jumping.
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10. Genetic "Junk" and Mutations
• Flaw: The genome is full of non-coding or redundant DNA and is prone to harmful mutations.
• Result: Genetic diseases, cancer, and congenital defects.
• Evolutionary Explanation: DNA accumulates "baggage" over time. There's no intelligent editing or streamlining process.
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11. Susceptibility to Cancer
• Flaw: Cells divide for life but are prone to mutations that cause cancer.
• Result: One of the top global causes of death.
• Evolutionary Explanation: Cell division is essential for life, but natural selection can't eliminate all cancer risk — especially after reproductive age.
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12. Human Psychology Biases
• Flaw: We are prone to cognitive biases (e.g., confirmation bias, tribalism, overconfidence).
• Result: Misjudgments, discrimination, and conflict.
• Evolutionary Explanation: These evolved to enhance survival in specific environments, not to produce truth-seeking rationality.
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If we were designed by an omnibenevolent, omniscient, and omnipotent being, such flaws are impossible to justify. Evolution by natural selection, on the other hand, explains these quirks and imperfections as the result of a messy, blind, trial-and-error process — where old parts are tweaked, not replaced, and survival/reproduction, not perfection, is the end goal.

[1213]

The existence of design flaws in living organisms is often cited as evidence for evolution by natural selection rather than intelligent design by an all-loving, all-knowing, and all-powerful deity. If such a being existed and created life intentionally, we might expect optimal design ...

Yes, I believe the design was optimal originally. But then people rejected God and degeneration begun.

10. Genetic "Junk" and Mutations
• Flaw: The genome is full of non-coding or redundant DNA and is prone to harmful mutations.
• Result: Genetic diseases, cancer, and congenital defects.
• Evolutionary Explanation: DNA accumulates "baggage" over time. There's no intelligent editing or streamlining process....

I think "genetic junk" is one of the best evidences for creation. It shows things were originally good and at one point started to degenerate.

[Compassionist]

The existence of design flaws in living organisms is often cited as evidence for evolution by natural selection rather than intelligent design by an all-loving, all-knowing, and all-powerful deity. If such a being existed and created life intentionally, we might expect optimal design ...

Yes, I believe the design was optimal originally. But then people rejected God and degeneration begun.

10. Genetic "Junk" and Mutations
• Flaw: The genome is full of non-coding or redundant DNA and is prone to harmful mutations.
• Result: Genetic diseases, cancer, and congenital defects.
• Evolutionary Explanation: DNA accumulates "baggage" over time. There's no intelligent editing or streamlining process....

I think "genetic junk" is one of the best evidences for creation. It shows things were originally good and at one point started to degenerate.

I disagree. You are entitled to your beliefs.

[A Freeman]

Excerpt below from:

https://med.stanford.edu/news/all-news/ ... eases.html

For decades, scientists have known that, despite its name, “junk DNA” in fact plays a critical role: While the coding genes provide blueprints for building proteins, which direct most of the body's functions, some of the noncoding sections of the genome, including regions previously dismissed as “junk,” seem to turn up or down the expression of those genes.

But it’s been unclear how certain noncoding regions influence gene-expression levels — that is, the number of times a gene is copied into RNA and used to make proteins.

Now, a new study by Polly Fordyce, PhD, associate professor of bioengineering and of genetics, and her colleagues has unraveled some of the mystery. Their discovery may help researchers understand complex genetic conditions, including autism, schizophrenia, cancer and Crohn’s disease.

"We've known for a while that short tandem repeats, or STRs, aren't junk because their presence or absence correlates with changes in gene expression," Fordyce said. "But we haven't known how they exert these effects."

Authors of the study, published Sept. 22 in Science, believe it's the first to offer a roadmap to understanding how STR changes can impact gene expression.

An evolving view of 'junk DNA'

STRs make up about 5% of the human genome. "Starting in the 1980s, researchers noticed that changes to these repetitive sequences can affect gene expression," said the study's lead author, Connor Horton, who was a technician in Fordyce's lab. "That's the trail of breadcrumbs we've followed."

For the study, the researchers looked at how STRs interact with proteins called transcription factors. Transcription factors attach to noncoding DNA, regulating the expression of protein-coding genes.

"Researchers have spent a lot of time characterizing these transcription factors and figuring out which sequences - called motifs - they like to bind to the most," Fordyce said. But current models don't adequately explain where and when transcription factors bind to noncoding DNA to regulate gene expression. Sometimes, no transcription factor is attached to something that looks like a perfect motif. Other times, transcription factors bind to stretches of DNA that aren't motifs.

[A Freeman]

Excerpt below from:

https://www.quantamagazine.org/the-comp ... -20210901/



The 98% of the human genome that does not encode proteins is sometimes called junk DNA, but the reality is more complicated than that name implies.

Samuel Velasco/Quanta Magazine
Introduction
Jake Buheler
By Jake Buehler

Contributing Writer

September 1, 2021
Abstractions blog
biology
DNA
explainers
genes
genome
molecular biology
RNA
All topics
(opens a new tab)

Imagine the human genome as a string stretching out for the length of a football field, with all the genes that encode proteins clustered at the end near your feet. Take two big steps forward; all the protein information is now behind you.

The human genome has three billion base pairs in its DNA, but only about 2% of them encode proteins. The rest seems like pointless bloat, a profusion of sequence duplications and genomic dead ends often labeled “junk DNA.” This stunningly thriftless allocation of genetic material isn’t limited to humans: Even many bacteria seem to devote 20% of their genome to noncoding filler.

Many mysteries still surround the issue of what noncoding DNA is, and whether it really is worthless junk or something more. Portions of it, at least, have turned out to be vitally important biologically. But even beyond the question of its functionality (or lack of it), researchers are beginning to appreciate how noncoding DNA can be a genetic resource for cells and a nursery where new genes can evolve.

“Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” said Cristina Sisu (opens a new tab), a geneticist at Brunel University London.

Scientists casually referred to “junk DNA” as far back as the 1960s, but they took up the term more formally in 1972, when the geneticist and evolutionary biologist Susumu Ohno used it to argue that large genomes would inevitably harbor sequences, passively accumulated over many millennia, that did not encode any proteins. Soon thereafter, researchers acquired hard evidence of how plentiful this junk is in genomes, how varied its origins are, and how much of it is transcribed into RNA despite lacking the blueprints for proteins.

Technological advances in sequencing, particularly in the past two decades, have done a lot to shift how scientists think about noncoding DNA and RNA, Sisu said. Although these noncoding sequences don’t carry protein information, they are sometimes shaped by evolution to different ends. As a result, the functions of the various classes of “junk” — insofar as they have functions — are getting clearer.

Cells use some of their noncoding DNA to create a diverse menagerie of RNA molecules that regulate or assist with protein production in various ways. The catalog of these molecules keeps expanding, with small nuclear RNAs (opens a new tab), microRNAs (opens a new tab), small interfering RNAs (opens a new tab) and many more. Some are short segments, typically less than two dozen base pairs long, while others are an order of magnitude longer. Some exist as double strands or fold back on themselves in hairpin loops. But all of them can bind selectively to a target, such as a messenger RNA transcript, to either promote or inhibit its translation into protein.

These RNAs can have substantial effects on an organism’s well-being. Experimental shutdowns of certain microRNAs in mice, for instance, have induced disorders ranging from tremors (opens a new tab) to liver dysfunction (opens a new tab).

By far the biggest category of noncoding DNA in the genomes of humans and many other organisms consists of transposons (opens a new tab), segments of DNA that can change their location within a genome. These “jumping genes” have a propensity to make many copies of themselves — sometimes hundreds of thousands — throughout the genome, says Seth Cheetham (opens a new tab), a geneticist at the University of Queensland in Australia. Most prolific are the retrotransposons (opens a new tab), which spread efficiently by making RNA copies of themselves that convert back into DNA at another place in the genome. About half of the human genome is made up of transposons (opens a new tab); in some maize plants, that figure climbs to about 90%.

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"We’re in a golden age of understanding noncoding DNA and noncoding RNA."

Zhaolei Zhang, University of Toronto

[A Freeman]

Excerpt below:

https://evolutionnews.org/2025/01/happy ... -junk-dna/

Happy New Year! No. 1 Story of 2024: Nobel Prize for Function of “Junk DNA”

What’s the biggest science story of the year? My vote goes to the 2024 Nobel Prize in Physiology or Medicine, awarded for the discovery of function for a type of “junk DNA” that produces microRNA (miRNA), a crucial molecule involved in gene regulation. That so-called genetic junk would turn out to be functional was a prediction of intelligent design going back to the 1990s. On that, ID has been vindicated over and over again, now by the Nobel Committee. Our colleagues Richard Sternberg and Bill Dembski were early predictors, as critics of what Jonathan Wells called in a 2011 book, The Myth of Junk DNA.

While David Coppedge broke the Nobel story for us back in October, it came up as I was traveling and I completely missed it. Last week I did a podcast on this year’s Nobel Prize (it’s below), and I realized what a huge story it is. Better late than never, let’s dig into what was discovered.

First, the official Nobel Prize press release explains:

The Nobel Assembly at Karolinska Institutet has today decided to award the 2024 Nobel Prize in Physiology or Medicine jointly to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation

This year’s Nobel Prize honors two scientists for their discovery of a fundamental principle governing how gene activity is regulated.

The information stored within our chromosomes can be likened to an instruction manual for all cells in our body. Every cell contains the same chromosomes, so every cell contains exactly the same set of genes and exactly the same set of instructions. Yet, different cell types, such as muscle and nerve cells, have very distinct characteristics. How do these differences arise? The answer lies in gene regulation, which allows each cell to select only the relevant instructions. This ensures that only the correct set of genes is active in each cell type.

Victor Ambros and Gary Ruvkun were interested in how different cell types develop. They discovered microRNA, a new class of tiny RNA molecules that play a crucial role in gene regulation. Their groundbreaking discovery revealed a completely new principle of gene regulation that turned out to be essential for multicellular organisms, including humans. It is now known that the human genome codes for over one thousand microRNAs. Their surprising discovery revealed an entirely new dimension to gene regulation. MicroRNAs are proving to be fundamentally important for how organisms develop and function.

[A Freeman]

Excerpt below from:

https://truthstodiefor.com/the-big-hoax ... after-all/

The Big Hoax: Turns Out ‘Junk’ DNA Isn’t Junk After All

"For decades, evolutionary scientists dismissed vast stretches of our DNA as useless “junk”—leftover evolutionary baggage with no purpose. This concept conveniently supported evolutionary theory while dismissing what creationists have long maintained: our genome reflects intelligent design, not random processes. Recent scientific discoveries have dramatically shifted the paradigm, revealing that what was once labelled “junk” actually serves critical functions in God’s intricate design."

THE RISE AND FALL OF “JUNK DNA”

The term “junk DNA” emerged in the 1970s to describe the approximately 98% of human DNA that doesn’t code directly for proteins. Evolutionists seized upon the concept, claiming these vast non-coding regions represented evolutionary debris—broken genes and viral remnants accumulated through millions of years of mutation and selection.

But as Scripture reminds us in Psalm 139:14, we’re “fearfully and wonderfully made.” Would our Creator, who designed the universe with such precision, fill our genetic code with meaningless garbage? Creationists didn’t think so, and science is now confirming this biblical wisdom.


MODERN SCIENCE REVEALS THE TRUTH

The scientific establishment received a wake-up call with the Encyclopaedia of DNA Elements (ENCODE) project. In 2012, ENCODE researchers shocked the scientific community by announcing approximately 80% of the human genome serves biochemical functions—a direct challenge to the “junk DNA” paradigm.

Here’s what researchers have discovered about regions formerly dismissed as “junk”:

- Regulatory Functions: Non-coding DNA contains thousands of enhancers and silencers that control when and where genes are expressed. These sophisticated “switches” are crucial for human development and cellular function.

- Structural Importance: Some non-coding DNA maintains chromosome structure and regulates DNA replication.

- RNA Production: Many non-coding regions produce RNA molecules that regulate gene expression, protect against viruses, and guide crucial cellular processes.

- Conservation Across Species: Many non-coding DNA sequences show remarkable conservation across different species – strong evidence they serve important functions worth preserving.

- 3D Genome Organisation: These regions help fold DNA into specific three-dimensional configurations necessary for proper gene expression.

Even transposable elements (once considered quintessential “junk”) are now understood to play crucial roles in immune function, brain development, and even pregnancy. As Tom Misteli, director of the Center for Cancer Research at the US National Cancer Institute, admitted: “I don’t think anyone would have anticipated even close to the level of precision and regulatory control that exists in the genome.”

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So, the ignorant and arrogant scientists who mistakenly labeled the part of the human genome that they didn't understand as "junk", have been proven wrong yet again, as always happens as science "evolves", i.e. comes to the realization of truth that DNA is a complex code, very obviously written by a super intelligent designer (aka our Creator).

[Compassionist]

Thank you very much for posting about Junk DNA not being junk. I learned something new. Science is self-correcting. That's what I love about science. Scientists are always trying to refine our knowledge and understanding. That's where it differs from religions.

What about all the other points I raised in my original post?

[Diagoras]

So, the ignorant and arrogant scientists who mistakenly labeled the part of the human genome that they didn't understand as "junk", have been proven wrong yet again, …

…by whom?

Scientists, it appears.

Your argument therefore looks very much like ‘cherry picking’.

[Diagoras]

Yes, I believe the design was optimal originally. But then people rejected God and degeneration begun.

<bolding mine>

If we are to accept the logic of that argument, then it follows that giraffes also rejected God.

1. God created all animals perfectly.
2. Modern giraffes have an anatomical flaw.

Conclusion: ????

Perhaps you can suggest what conclusion makes most sense.