'Bad Design' Objections: The Eye, the Laryngeal Nerve and Junk DNA

The "bad design" objection turns the argument for design around. If a wise Creator made living things, critics ask, why does the human retina place its wiring in front of the light-sensitive cells? Why does a nerve for the voice box run down into the chest and loop back up, a detour of several meters in a giraffe? Why do we carry an appendix that can kill us, and a genome full of what was once called "junk"?

These questions deserve a straight answer. Some examples have aged badly; others still carry real force as evidence of shared history. All of them, when aimed at God, depend on a premise that is theological, not scientific: that we know what God would and would not do. This article takes the best-known cases one at a time, gives the critics' case in their own words, grades each reply honestly, and then sets out what the Orthodox Church teaches about a good creation that now "groans and labors with birth pangs" (Romans 8:22, NKJV).

In brief

The "bad design" objection has two forms. As a scientific argument it says that odd structures are best explained by descent with modification. As an argument against God it says that no wise designer would have made them. The scientific form has real weight in some cases: the recurrent laryngeal nerve follows a path fixed early in vertebrate embryonic development and shared by all living land vertebrates. The anti-God form fails, because it assumes knowledge of a Creator's purposes that no one has, as the philosopher Elliott Sober, himself a critic of Intelligent Design, has argued. Several of the standard examples have also weakened. The inverted retina has measured optical and metabolic advantages, including Müller cells that guide light to the photoreceptors. The appendix is now thought to have immune functions. The ENCODE project's claim that 80 percent of the genome is functional was overstated, but so was the older confidence that most non-coding DNA is useless. Christians need not claim that every structure is optimal. The Church confesses a creation made "very good" (Genesis 1:31) and now "subjected to futility" (Romans 8:20) through man's fall, awaiting renewal in Christ.

Thesis: "Bad design" arguments can count as evidence about the history of living things, but they cannot show that there is no Creator, and several of the best-known examples rest on a misreading of the biology.

Two arguments under one name

The objection is as old as Darwin. In the closing chapter of On the Origin of Species (1859) he wrote: "On the view of each organic being and each separate organ having been specially created, how utterly inexplicable it is that parts, like the teeth in the embryonic calf or like the shrivelled wings under the soldered wing-covers of some beetles, should thus so frequently bear the plain stamp of inutility!"¹

Two claims are bundled together here. The first is historical: structures that look like modified versions of older structures point to common descent. The biologist Kenneth Miller, a Roman Catholic and one of Intelligent Design's leading critics, stated it precisely in 1994: "the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification. A designed organism should not."² The second claim is theological: a Creator would not have made things this way. The evolutionary biologist Francisco Ayala pressed it in 2007: "The design of organisms is not intelligent but imperfect and, at times, outright dysfunctional."³ The first claim can be weighed with evidence. The second needs a premise about God that biology cannot supply.

The eye: wired backwards?

The objection

In the vertebrate retina the light-sensitive rods and cones sit at the back. Light must pass through layers of nerve cells and blood vessels to reach them, and the nerve fibers exit through the retina at one point, leaving a blind spot. Miller wrote: "No one, for example, would suggest that the neural wiring connections should be placed on the side that faces the light, rather than on the side away from it. Incredibly, this is exactly how the human retina is constructed." The eyes of the squid and octopus, he noted, are "wired right-side-out, with no light-scattering nerve cells or blood vessels above the photoreceptors and no blind spot."⁴ To his credit he added: "None of this should be taken to suggest that the eye functions poorly." His argument concerned the structural plan, not performance (compare the site's infographic The Human Eye Is an Integrated System).

What research has found since

Three lines of work have changed the picture. First, the arrangement has a metabolic logic. The photoreceptors face the retinal pigment epithelium (RPE), a layer of cells behind them. In a 2007 review of eye evolution, the vision scientists Trevor Lamb, Shaun Collin and Edward Pugh noted that the RPE cells "isomerize the chromophore retinal to its 11-cis form and synthesize melanin, which helps to attenuate unwanted light," and that in the inverted position they no longer occupy the photoreceptor layer, "so that more of the light can be captured. These factors might help to explain the inverted nature of the vertebrate retina."⁵

Second, the layers in front are not simply in the way. In 2007 Kristian Franze and colleagues reported that Müller glial cells, which span the retina, act as optical fibers: "Müller cells seem to mediate the image transfer through the vertebrate retina with minimal distortion and low loss."⁶ In 2014 Amichai Labin and colleagues, combining a computational model of the human retina with imaging of guinea pig retinas, found that Müller cells concentrate green-red light onto cones while letting blue-violet light reach the surrounding rods, raising photon absorption by human middle- and long-wavelength cones "by a factor of ~7.5" at a modest cost to rods. This, they concluded, "provides a mechanism to improve cone-mediated day vision, with minimal interference with rod-mediated night vision."⁷

Third, the layout saves space. Ronald Kröger and Oliver Biehlmaier argued in 2009 that "the inverted retina actually is a superior space-saving solution, especially in small eyes."⁸ Design advocates had argued along similar lines earlier. George Ayoub, writing in the design journal Origins & Design, held that "there are excellent functional reasons for vertebrate photoreceptors to be oriented as they are," pointing to the RPE, which "recycles photopigments, removes spent outer segments of the photoreceptors, provides an opaque layer to absorb excess light, and performs additional functions."⁹

Grading the reply

The reply is good but not complete. The blind spot is real, and the Labin paper itself calls the arrangement "seemingly reverse," one "expected to cause blurring of the image." A critic can call Müller cells a workaround; a defender can answer that a structure with documented benefits is not a blunder. {{strong: The inverted retina has measured advantages that the classic objection did not take into account, though its costs, such as the blind spot, are also real.}} The evidence does not support the confident claim that the vertebrate eye is simply badly built.

The recurrent laryngeal nerve

The objection

The recurrent laryngeal nerve branches from the vagus nerve in the chest, hooks under a great vessel (the aortic arch on the left, the subclavian artery on the right) and climbs back up the neck to the larynx. Mathew Wedel's 2012 paper "A monument of inefficiency" explains why: "The nerve appears early in embryonic development, before the pharyngeal and aortic arches are separated by the development of the neck." The path is "shared by all extant tetrapods." In the tallest giraffes the route from brainstem to larynx "approaches 5 m," and the nerve "is frequently cited as the kind of post-hoc evolutionary kludge (= workaround) that an intelligent designer would surely have avoided," Wedel notes, citing among others Jerry Coyne and Richard Dawkins.¹⁰

The design reply

Casey Luskin of the Discovery Institute replied in 2010 with two arguments. First, the nerve does more than serve the larynx. He quoted Gray's Anatomy: as the nerve hooks around the artery "it gives off several cardiac filaments to the deep part of the cardiac plexus," and in the neck it sends branches to the esophagus and trachea.¹¹ Second, and more basic, he quoted a design-friendly biologist: "this is only a problem for design if one assumes design means designed from scratch for each taxon, and if one believes that the designer would necessarily use the shortest distance between two points (in other words, that the designer thinks like we do), and that there are not other design considerations at play."¹²

Grading the reply

Honesty requires a split verdict. The first argument is weak. The branches are real, but they do not explain why the fibers bound for the larynx descend into the chest, while the superior laryngeal nerve takes a short, direct path. Wedel records that a non-recurrent nerve occurs on the right side "in less than 1% of humans," tied to an abnormal artery, and that in the giraffe the long route "is compensated to some extent by larger, more heavily myelinated nerve fibers."¹³ A direct route is anatomically possible; the developmental plan does not take it.

The second argument is stronger. The nerve's path shows a developmental plan shared across land vertebrates, and it fits common descent well. But it shows only that the Creator, if He worked through that history, did not redraw each animal from a blank page. {{strong: The recurrent laryngeal nerve's looping path follows from how the vertebrate embryo forms the neck and great vessels, and it is shared by all living land vertebrates.}} As evidence against God, it proves nothing. (On the range of Orthodox views about common descent, see Can a Christian Accept Evolution?)

The appendix

Darwin called "the vermiform appendage of the caecum" a rudiment and wrote in The Descent of Man: "Not only is it useless, but it is sometimes the cause of death."¹⁴ In 2007 a Duke University team (R. Randal Bollinger, William Parker and colleagues) proposed instead that "the human appendix is well suited as a 'safe house' for commensal bacteria," able to re-inoculate the gut after an illness purges it.¹⁵ Heather Smith's 2023 review reports that "the cecal appendix has evolved independently numerous times throughout mammalian evolution, significantly more than would be expected due to chance alone, suggesting that the appendix is adaptively advantageous," while saying with care that it "may serve important protective functions."¹⁶

One caution keeps this honest: evolutionary biologists reply that an organ reduced from an ancestral form can keep or gain other uses, so a function does not by itself refute their account. {{moderate: The human appendix appears to have immune and protective functions, though how much it matters to health today is still being studied.}} Darwin's verdict that it is "useless," however, has not stood.

Junk DNA, briefly

In 2012 the ENCODE consortium reported that its data "enabled us to assign biochemical functions for 80% of the genome."¹⁷ Dan Graur and colleagues replied in 2013 that ENCODE's loose definition of function led to an "absurd conclusion."¹⁸ Most current estimates of the functional fraction are far lower, though some sequences once written off have proved active. The site's full treatment is Junk DNA, ENCODE, and the Design Debate. Neither "junk, therefore no God" nor "no junk, therefore design" follows.

What the objection assumes about God

Elliott Sober, a philosopher of biology at the University of Wisconsin, is no friend of Intelligent Design. Yet in a 2007 paper in The Quarterly Review of Biology he argued that the imperfection objection fails. A summary of the paper puts it plainly: the "no designer worth his salt" argument "assumes the designer would want pandas to have better eating implements, but the objection has no justification for this assumption."¹⁹ Sober then turned the point against design arguments: "If imperfect adaptations do not demonstrate that the mini-ID claim is false, perhaps the right criticism is that this statement cannot be tested." That second step needs its own answer. The first is sound: to say that God would not have done it this way, one must know what God intends. Scripture says otherwise: "For My thoughts are not your thoughts" (Isaiah 55:8, NKJV).

The Fathers did not treat creation as a machine tuned to one measure of efficiency. St Basil the Great, preaching on the plants of the third day, insisted that "not a single thing has been created without reason, not a single thing is useless," and gave the example of hemlock, poison to us but food for the starling.²⁰ Basil spoke of whole creatures, not genes or nerve paths. His point is theological: usefulness is not measured only by usefulness to us. The objection is, at bottom, the problem of evil applied to anatomy, a real question the site answers in If God Exists, Why Is There So Much Evil and Suffering? Christianity does not answer it by denying the frailty.

A creation subjected to futility

The Orthodox Church does not teach that the world we now see is creation as God first willed it. The Septuagint Book of Wisdom says: "For God made not death: neither hath he pleasure in the destruction of the living," and "through envy of the devil came death into the world" (Wisdom 1:13; 2:24, Brenton).²¹ St Paul writes that "the creation was subjected to futility, not willingly, but because of Him who subjected it in hope" (Romans 8:20, NKJV).

St John Chrysostom read the passage as binding the whole created order to man's fall: "What is the meaning of, the creation was made subject to vanity? Why that it became corruptible. For what cause, and on what account? On account of you, O man."²² St Basil said that at its creation "the rose was without thorns," and that the thorn now reminds us "of our sin, which condemned the earth to produce thorns and caltrops."²³

This must be stated carefully. It is the Church's teaching that death and corruption are not God's original intention, and that through the sin of our first parents mankind inherited mortality and corruption, not Adam's personal guilt (see Original Sin vs. Ancestral Sin). It is not a defined dogma that the Fall rerouted a particular nerve, and Orthodox writers differ on how the fall of creation relates to the long history the fossil record shows. Basil's thorn is a homily's image, not a botanical claim. So an honest Orthodox answer does not use the Fall as a scientific explanation for any given structure. It uses it as Scripture does: a world of decay is not the last word about God's work, and creation groans because it awaits its healing in Christ, whose Resurrection is the first fruits of a renewed creation. That answer rejects the atheist conclusion that frailty disproves the Creator, and it rejects the pretense that every structure in a mortal world must be flawless.

Grading the answers

Objection	Best reply	Our grade
The retina is wired backwards	Müller cells guide light; the RPE sustains the photoreceptors; the layout saves space	Strong against "badly built"; the blind spot is a real cost
The laryngeal nerve's detour	It also supplies heart, trachea and esophagus	Weak
The laryngeal nerve's detour	A shared developmental plan does not exclude a Creator	Strong against atheism; concedes common descent
The appendix is useless	Immune tissue; possible reservoir for gut bacteria	Moderate to strong
The genome is mostly junk	Some "junk" has proved functional	Moderate; the 80 percent claim was overstated
No wise God would make this world	We do not know God's purposes; creation is subject to corruption	Strong; granted even by Sober

The strongest objections

"Every flaw becomes 'unknown purposes' or 'the Fall.' That explains everything and therefore nothing."

This is a fair warning, and it is why this article grades the replies instead of declaring victory. Where the evidence favors common descent, as with the laryngeal nerve, the article says so. The Christian claim is not that every structure is optimal. It is that God's existence is not settled by the efficiency of a nerve; it is known from the existence and order of the world, the moral law, and above all the Resurrection of Christ (see Is Intelligent Design a "God of the Gaps" Argument?).

"The octopus eye proves a better design was possible."

It proves that a camera eye can be built the other way round. It does not prove that the vertebrate arrangement is worse overall, since the two eyes are different systems with different trade-offs, and the space-saving advantage applies most to small eyes.

"If God used common descent, design is an empty word."

Only if design means a series of separate interventions. For the Fathers, God is the Maker of all things whose providence sustains every process, not one more cause competing with nature. Orthodox Christians hold a range of views on how God created; that He is the Creator is the faith of the Church.

What we can say confidently

• The "bad design" objection mixes a scientific claim (common descent) with a theological claim (God would not have done it this way).
• The vertebrate retina has measured optical, metabolic and spatial advantages.
• The recurrent laryngeal nerve follows a developmental path shared by all living land vertebrates; its branches to other organs do not explain the detour.
• Researchers no longer regard the appendix as simply useless.
• Even critics of Intelligent Design such as Elliott Sober reject the argument that imperfection refutes a designer.

What remains disputed

• Whether the inverted retina is, on balance, as good as the everted arrangement or a well-compensated historical constraint.
• How much the appendix matters to health today.
• What fraction of the human genome is functional.
• Whether bad-design examples count against Intelligent Design specifically, as opposed to counting for common descent.
• Among Orthodox writers, how the fall of creation in Romans 8 relates to the history of life before humanity.

Conclusion

The "bad design" argument tells us something true: living things carry the marks of history, and some of them are frail. It does not tell us what its atheist users want it to say. A nerve that loops around the heart is a fact about embryology; the claim that no God would allow it is a guess about God. On the eye and the appendix, the confident verdicts of an earlier generation have not held up.

The Orthodox Christian can look at all of this without fear. The Creed confesses the Father Almighty, "Maker of Heaven and Earth and of all things visible and invisible." Scripture does not describe a world without thorns; it describes a good creation, wounded by sin and subjected to futility "in hope." The answer to its groaning is not a better-engineered nerve but the risen Christ, in whom "the creation itself also will be delivered from the bondage of corruption" (Romans 8:21, NKJV).

Notes

1. Charles Darwin, On the Origin of Species (London: John Murray, 1859), ch. 14, Project Gutenberg eBook #1228 (first edition).
2. Kenneth R. Miller, "Life's Grand Design," Technology Review 97, no. 2 (February/March 1994): 24-32, text at http://www.millerandlevine.com/km/evol/lgd/index.html.
3. Francisco J. Ayala, "Darwin's greatest discovery: Design without designer," Proceedings of the National Academy of Sciences 104, suppl. 1 (2007): 8567-8573, doi:10.1073/pnas.0701072104.
4. Miller, "Life's Grand Design" (see note 2).
5. Trevor D. Lamb, Shaun P. Collin and Edward N. Pugh Jr., "Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup," Nature Reviews Neuroscience 8 (2007): 960-976, doi:10.1038/nrn2283 (author manuscript, PMC3143066).
6. Kristian Franze et al., "Müller cells are living optical fibers in the vertebrate retina," Proceedings of the National Academy of Sciences 104, no. 20 (2007): 8287-8292, doi:10.1073/pnas.0611180104.
7. Amichai M. Labin, Shadi K. Safuri, Erez N. Ribak and Ido Perlman, "Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision," Nature Communications 5 (2014): 4319, doi:10.1038/ncomms5319.
8. Ronald H. Kröger and Oliver Biehlmaier, "Space-saving advantage of an inverted retina," Vision Research 49 (2009): 2318-2321, doi:10.1016/j.visres.2009.07.001 (abstract).
9. George Ayoub, "On the Design of the Vertebrate Retina," Origins & Design 17, no. 1, as quoted in Casey Luskin, "National Geographic Evolution Article Discusses Evidence that Supports Intelligent Design (Part III)," Discovery Institute, 18 November 2006, https://scienceandculture.com/2006/11/national_geographic_evolution/.
10. Mathew J. Wedel, "A monument of inefficiency: The presumed course of the recurrent laryngeal nerve in sauropod dinosaurs," Acta Palaeontologica Polonica 57, no. 2 (2012): 251-256, doi:10.4202/app.2011.0019.
11. Casey Luskin, "The Recurrent Laryngeal Nerve Does Not Refute Intelligent Design," Discovery Institute, 14 October 2010, https://scienceandculture.com/2010/10/the_recurrent_laryngeal_nerve_/, quoting Gray's Anatomy (the 1918 twentieth U.S. edition has the same wording).
12. Luskin, "The Recurrent Laryngeal Nerve" (see note 11).
13. Wedel, "A monument of inefficiency," 252-253 (see note 10).
14. Charles Darwin, The Descent of Man, 2nd ed. (London: John Murray, 1874), ch. 1, Project Gutenberg eBook #2300.
15. R. Randal Bollinger et al., "Biofilms in the large bowel suggest an apparent function of the human vermiform appendix," Journal of Theoretical Biology 249 (2007): 826-831, doi:10.1016/j.jtbi.2007.08.032 (abstract).
16. Heather F. Smith, "A review of the function and evolution of the cecal appendix," The Anatomical Record 306 (2023): 972-982, doi:10.1002/ar.24917 (abstract).
17. ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature 489 (2012): 57-74, doi:10.1038/nature11247.
18. Dan Graur et al., "On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE," Genome Biology and Evolution 5 (2013): 578-590, doi:10.1093/gbe/evt028.
19. Elliott Sober, "What Is Wrong with Intelligent Design?" The Quarterly Review of Biology 82, no. 1 (2007): 3-8. Summary: "What Is Wrong With Intelligent Design?" ScienceDaily, 23 February 2007, https://www.sciencedaily.com/releases/2007/02/070222155420.htm; Sober's sentence as quoted in "Elliott Sober: What is wrong with Intelligent Design?" The Panda's Thumb, 19 February 2007, https://pandasthumb.org/archives/2007/02/elliott-sober-w.html.
20. St Basil the Great, Hexaemeron, Homily 5.4, trans. Blomfield Jackson, NPNF2 vol. 8, https://www.newadvent.org/fathers/32015.htm.
21. Wisdom of Solomon 1:13; 2:23-24, Brenton Septuagint translation, https://ebible.org/eng-Brenton/WIS01.htm and WIS02.htm.
22. St John Chrysostom, Homily 14 on Romans, trans. J. Walker, J. Sheppard and H. Browne, rev. George B. Stevens, NPNF1 vol. 11, https://www.newadvent.org/fathers/210214.htm.
23. St Basil the Great, Hexaemeron, Homily 5.6 (see note 20).

Bibliography

Primary sources

• The Holy Bible, New King James Version. Nashville: Thomas Nelson, 1982. Brenton, Lancelot C. L., trans. The Septuagint with Apocrypha: English. London: Samuel Bagster, 1851.
• Darwin, Charles. On the Origin of Species. London: John Murray, 1859. And The Descent of Man. 2nd ed. London: John Murray, 1874.

Orthodox and patristic sources

• Basil the Great. Hexaemeron. Trans. Blomfield Jackson. Nicene and Post-Nicene Fathers, Second Series, vol. 8. Buffalo: Christian Literature Publishing Co., 1895.
• John Chrysostom. Homilies on Romans. Nicene and Post-Nicene Fathers, First Series, vol. 11. Buffalo: Christian Literature Publishing Co., 1889.

Other scholarship (including scholars who disagree)

• Ayala, Francisco J. "Darwin's greatest discovery: Design without designer." PNAS 104, suppl. 1 (2007): 8567-8573.
• Bollinger, R. Randal, et al. "Biofilms in the large bowel suggest an apparent function of the human vermiform appendix." Journal of Theoretical Biology 249 (2007): 826-831.
• ENCODE Project Consortium. "An integrated encyclopedia of DNA elements in the human genome." Nature 489 (2012): 57-74.
• Franze, Kristian, et al. "Müller cells are living optical fibers in the vertebrate retina." PNAS 104 (2007): 8287-8292.
• Graur, Dan, et al. "On the immortality of television sets." Genome Biology and Evolution 5 (2013): 578-590.
• Kröger, Ronald H., and Oliver Biehlmaier. "Space-saving advantage of an inverted retina." Vision Research 49 (2009): 2318-2321.
• Labin, Amichai M., et al. "Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision." Nature Communications 5 (2014): 4319.
• Lamb, Trevor D., Shaun P. Collin and Edward N. Pugh Jr. "Evolution of the vertebrate eye." Nature Reviews Neuroscience 8 (2007): 960-976.
• Miller, Kenneth R. "Life's Grand Design." Technology Review 97, no. 2 (1994): 24-32.
• Smith, Heather F. "A review of the function and evolution of the cecal appendix." The Anatomical Record 306 (2023): 972-982.
• Sober, Elliott. "What Is Wrong with Intelligent Design?" The Quarterly Review of Biology 82 (2007): 3-8.
• Wedel, Mathew J. "A monument of inefficiency." Acta Palaeontologica Polonica 57 (2012): 251-256.

Sources from the tradition discussed (Intelligent Design)

• Luskin, Casey. "National Geographic Evolution Article Discusses Evidence that Supports Intelligent Design (Part III)." Discovery Institute, 2006 (quoting George Ayoub, "On the Design of the Vertebrate Retina," Origins & Design 17, no. 1).
• Luskin, Casey. "The Recurrent Laryngeal Nerve Does Not Refute Intelligent Design." Discovery Institute, 2010.