Light, Wombs, and Signs: Opsin Genes, the 2026 Nobel Prize, Placental Gene Co-option, and the Qur’anic Theme of Night and Day

Presented by Claude for Zia H Shah MD

Abstract

This essay follows one idea, old things put to new and better uses, through four subjects. The first is the 2026 Nobel Prize, which honored placing an algal light-sensitive protein into nerve cells. The second is the full range of natural opsins, microbial (type I) and animal (type II), including a correction of the misconception that one family descends from the other. The third is the mammalian placenta, built in large part from captured viral and transposon DNA. The fourth is the Qur’an’s call to reflect on night and day as signs for ulu’l-albab, people of understanding, given here in full Arabic and linked to circadian physiology. Drawing on Zia H. Shah MD’s writings at The Glorious Quran and Science (thequran.love), the essay argues that this growing list of recycled genes is consistent with, and for the theist suggestive of, guided evolution. Throughout, it states fairly how mainstream biology explains the same data.

Corrections and Verifications of the Working Notes

Claim in notes	Verdict	Evidence
2026 laureates: Deisseroth, Hegemann, Nagel, for light-gated ion channels/optogenetics	Correct	Citation: “for their discoveries concerning light-gated ion channels and optogenetics”; announced 5 October 2026; 12 million SEK shared equally nobelprize
Algal optogenes became human eye/brain opsins	Incorrect	Type I and type II rhodopsins share a 7-transmembrane, lysine–retinal Schiff-base design but “share no detectable sequence homology.” Most reviews favor convergence; a minority argue for very deep homology annualreviews
Animal opsins arose from melatonin-receptor-like GPCRs	Supported hypothesis	Feuda et al. (PNAS 2012) found that opsins share a common ancestor with melatonin receptors. The earliest steps are still debated nih
Mammals lost RH2, VA, parapinopsin, parietopsin, OPN4x	Correct	Borges et al. (BMC Genomics 2018), 154 mammals; attributed to a nocturnal bottleneck >215.5 million years ago springer
OPN5 highly conserved, OPN4 more variable	Correct	Upton et al. (J Biol Rhythms 2021): OPN5 and rhodopsin show “extreme conservation”; OPN4 is the most diverse mammalian opsin doi
~9 million extant life forms	Approximately correct	The most-cited estimate (Mora et al., PLoS Biology 2011) is ~8.7 million eukaryotic species; prokaryotes are excluded and far less certain
Neo-Darwinism says evolution is “random and blind”	Needs nuance	“Random” means mutations arise without regard to usefulness, not that outcomes are uncaused. thequran Selection is non-random

1. The 2026 Nobel Prize in Physiology or Medicine

Laureates and citation

On 5 October 2026 the Nobel Assembly at Karolinska Institutet awarded the prize jointly to Karl Deisseroth, Peter Hegemann and Georg Nagel “for their discoveries concerning light-gated ion channels and optogenetics.” nobelprize Each laureate holds a one-third share of the 12 million Swedish kronor. nobelprize nobelprize The press release describes optogenetics as “a method that makes it possible to show how nerve cells shape memories, feelings and behaviours in the living brain.” Committee chair Per Svenningsson said: “Optogenetics provides opportunities for mapping the brain in a way that we could once only dream of.” The release adds that “in clinical medicine, researchers are using the method in attempts to restore sight in people with visual impairment.” nobelprize

Deisseroth, 54, is a professor of bioengineering and of psychiatry and behavioral sciences at Stanford and an HHMI investigator. Hegemann, 71, is a professor of experimental biophysics at Humboldt University. Nagel, 73, is a professor of neurophysiology at the University of Würzburg. genengnews scmp The prize-winning discoveries were made at the Max Planck Institutes for Biochemistry (Martinsried) and Biophysics (Frankfurt). nature nobelprize Committee secretary Thomas Perlmann said all three called the others “my friends.” statnews Committee member Abdel El Manira traced the concept to Francis Crick’s suggestion that light might control specific cells, an idea that “seemed entirely far-fetched.” Scientific American Scientific American, STAT, CNN, C&EN, CBC, Al Jazeera, GEN and WBUR/NPR’s Here & Now confirm these details.

What a channelrhodopsin is

Chlamydomonas reinhardtii, a single-celled green alga, steers toward light using an “eyespot.” The eyespot’s photoreceptors turned out to be ion channels that open directly when their retinal chromophore absorbs a photon. Channelrhodopsin-2 (ChR2) is “a light-gated ion channel, which is native to the eyespot of the unicellular alga Chlamydomonas reinhardtii,” built on a seven-transmembrane-helix motif. pnas The Nobel Committee’s popular summary is titled “Light-seeking algae gave us a switch for nerve cells.” nobelprize

Timeline

2002. Nagel, Hegemann and colleagues published “Channelrhodopsin-1: A Light-Gated Proton Channel in Green Algae” (Science 296:2395–2398). uspto GEN notes that the Hegemann lab coined the name ChR1. genengnews
2003. Nagel et al. published “Channelrhodopsin-2, a directly light-gated cation-selective membrane channel” (PNAS 100:13940–13945). pnas They showed that the protein generates light-driven currents in human and hamster cells. cbc The Nobel summary notes that ChR2 “reacted exceptionally strongly and rapidly to a pulse of light.” nobelprize
2005. Boyden, Zhang, Bamberg, Nagel and Deisseroth published “Millisecond-timescale, genetically targeted optical control of neural activity” (Nature Neuroscience 8:1263–1268). Using “lentiviral gene delivery in combination with high-speed optical switching,” they achieved “reliable, millisecond-timescale control of neuronal spiking.” nature Nagel supplied the construct. genengnews The same year, Nagel’s group triggered rapid behavior in C. elegans with ChR2. pnas
2006. The field was named optogenetics. cbc
Later. Working with others, Deisseroth “used optogenetics to wake sleeping mice in a controlled manner.” nobelprize For sleep medicine this was a landmark: it showed causally that specific arousal circuits flip sleep into wakefulness.

How optogenetics works

Choose a microbial opsin gene. Options include ChR2 (blue, excitatory), red-shifted ChrimsonR (~590 nm, amber), or inhibitory pumps and anion channels.
Deliver it with a viral vector. Lentivirus was used in 2005; adeno-associated virus (AAV) is used clinically. A cell-type-specific promoter restricts expression to the chosen neurons.
Rely on the tissue’s own chromophore. Microbial opsins bind all-trans-retinal, which mammalian tissue already supplies.
Deliver light. Fibers, LEDs or goggles provide it. The retinal isomerizes, the channel opens, cations flow in, and the neuron fires within milliseconds. Inhibitory opsins silence neurons the same way.
Read out causation. Behavior, electrophysiology or imaging then show what the circuit actually does.

Medical applications

Retinitis pigmentosa. Sahel, Roska and colleagues (Nature Medicine 2021) treated a 58-year-old man diagnosed 40 years earlier. technologynetworks They injected AAV2.7m8-CAG-ChrimsonR-tdTomato into his worse eye and paired it with goggles that project the scene as amber light. technologynetworks gensight-biologics A patient who had only light perception could then locate and reach for objects, and EEG showed object-related visual-cortex activity. nature h1 It was “the first reported case of partial functional recovery in a neurodegenerative disease after optogenetic therapy” (PIONEER trial, NCT03326336; GS030, GenSight Biologics). nature +2 With one patient and partial recovery, this is a proof of principle.
Parkinson’s disease, epilepsy and psychiatry. In animals, optogenetics has been used to dissect how deep-brain stimulation works, to stop seizures with closed-loop light, and to map circuits for depression, anxiety, addiction and reward. These uses remain mostly research and target-finding.
Sleep medicine. Optogenetic dissection of hypocretin/orexin and hypothalamic–brainstem nodes has reshaped models of how sleep and wake switch, which is relevant to narcolepsy and insomnia.

2. The Natural Opsins

Two families, one architecture

Microbial (type I) rhodopsins occur in archaea, bacteria, algae, fungi and giant viruses. They work as light-driven pumps, channels or sensors, and their retinal isomerizes from all-trans to 13-cis. nih researchgate
Animal (type II) opsins occur only in animals. They are GPCRs or photoisomerases; in visual pigments, light isomerizes 11-cis retinal to all-trans. nih researchgate

Both have seven transmembrane helices and a lysine in helix 7 that binds retinal through a Schiff base (Lys296 in bovine numbering). biorxiv +2 Yet the Annual Review of Microbiology states that “microbial and animal rhodopsins share no detectable sequence homology.” This “has been attributed either to a deep divergence between two evolutionarily related families of transmembrane proteins or to convergent evolution.” annualreviews Kojima and Sudo (RSC Advances 2023) conclude that they “have convergently evolved from their distinctive origins.” rsc semanticscholar Ernst et al. (Chemical Reviews 2014) remain agnostic (“it is not clear whether microbial rhodopsins and animal rhodopsins have a common ancestry”) and mention an exon-shuffling hypothesis. acs

What follows: the Nobel-winning algal gene did not become our visual pigment. The more accurate and more striking point is that nature arrived at the same molecular answer at least twice, from different starting materials: seven helices, one lysine, one retinal.

Microbial (type I) rhodopsins

Rhodopsin	Source	Function
Bacteriorhodopsin	Halobacterium salinarum	Outward proton pump (found 1971)
Halorhodopsin	Haloarchaea	Inward chloride pump; NpHR silences neurons
Sensory rhodopsins I/II	Haloarchaea	Phototaxis sensors
Proteorhodopsin	Marine bacteria	Proton pump; widespread ocean light-harvesting
Xanthorhodopsin	Salinibacter ruber	Proton pump with carotenoid antenna
Channelrhodopsins (ChR1, ChR2, Chrimson)	Green algae	Light-gated cation channels (the Nobel tools)
Anion channelrhodopsins (GtACRs)	Cryptophyte algae	Light-gated chloride channels; inhibitory tools
Enzymerhodopsins	Fungi, choanoflagellates	Rhodopsin–cyclase fusions
Heliorhodopsins	Bacteria, archaea, algae, viruses	Reversed orientation; function unclear

The nine human opsin genes

Gene	Protein	Peak (approx.)	Location	Function
OPN1SW	S-cone opsin	~420 nm	S cones	Blue colour vision; early circadian input
OPN1MW	M-cone opsin	~530 nm	M cones	Trichromacy (X-linked)
OPN1LW	L-cone opsin	~558 nm	L cones	Trichromacy (primate duplication)
RHO	Rhodopsin	~500 nm	Rods	Dim-light vision; mutated in many retinitis pigmentosa cases
OPN3	Encephalopsin	Short-λ, poorly defined	Brain, retina, skin, vessels, immune cells	Negative regulator of melanogenesis; smooth-muscle and wound-healing roles sciencedirect biorxiv
OPN4	Melanopsin	~480 nm	ipRGCs (~1% of RGCs), iris	Circadian entrainment, pupil reflex, melatonin suppression
OPN5	Neuropsin	~380 nm (UVA)	Retina, hypothalamus, cornea, skin, testis	Local retinal/corneal entrainment; the only human UV opsin nih
RGR	RPE-retinal GPCR	Photoisomerase	RPE, Müller glia	Chromophore regeneration springer nih
RRH	Peropsin	Photoisomerase-like	RPE, Müller glia	Retinoid processing

Melanopsin and sleep medicine

In 2002, Berson, Dunn and Takao (Science 295:1070–1073) showed that “retinal ganglion cells innervating the SCN are intrinsically photosensitive,” and Hattar et al. (Science 295:1065–1070) described these “melanopsin-containing retinal ganglion cells.” The melanopsin protein itself was first reported earlier, by Provencio et al. in 1998. Melanopsin responds most strongly near 480 nm and lies in ipRGCs that project directly to the suprachiasmatic nucleus (SCN). Other ipRGC targets are the olivary pretectal nucleus (pupillary reflex), the ventrolateral preoptic nucleus (sleep) and thalamic regions. sciencedirect Through the SCN, ipRGC input confines melatonin to the subjective night and acutely suppresses it under bright light. pitt In humans exposed for long periods, the action spectra for melatonin suppression and phase resetting “were best fit by a single-opsin template with lambda_max at 481 and 483 nm,” with S-cones contributing early (PNAS 2022). pnas In older adults, melanopsin’s share of the response falls (J Pineal Res 2024). wiley The practical consequences:

Morning light advances the clock.
Evening blue-rich screens delay it.
Chromatic pupillometry can probe the melanopsin pathway in neurodegenerative disease. clinicaltrials

Outside the eye, OPN3 is consistently expressed in human skin, OPN3–OPN5 in the human iris, and corneal OPN5 rises after wounding. springer +2 Many extraocular functions still rest on animal or cell-culture data.

The nocturnal bottleneck

Borges et al. (BMC Genomics 2018) found that amphibians, reptiles and birds have 16, 17 and 15 opsin genes, while mammals have 10. RH2, VA, PARA (parapinopsin), PARIE (parietopsin) and OPN4x are absent “in all mammals,” springer which suggests “a global nocturnal bottleneck that explains the loss of these genes in the emerging lineage (>>215.5 million years ago).” springer The idea goes back to Walls (1942). nih The loss of pineal opsins tracks the reduction of the “third eye,” and the loss of OPN4x reflects a simplified circadian system that depends on retinal OPN4m. springer A frog study offers a complementary developmental hypothesis: mammals, birds and squamates develop in the dark of a womb or egg. oup

Conservation and Lys296

Upton et al. (J Biol Rhythms 2021) found that “OPN5 and rhodopsin show extreme conservation across all mammalian lineages,” whereas RGR and OPN4 “have high sequence diversity within mammals.” OPN5 is “the most conserved mammalian opsin,” and its monostable form likely arose in eutherians. doi OPN3 retains Lys296 and the acidic counter-ion, the molecular signature of a working photopigment. annualreviews

Origins

Feuda et al. (PNAS 2012) found that “the opsins share a common ancestor with the melatonin receptors.” nih The first opsin arose by duplication in an early eumetazoan and “might not have been light-sensitive.” Later duplications produced the C, R and Go/RGR subfamilies. harvard Placozoan “placopsins” lack the retinal-binding lysine. oup oup One proposed scenario is that a retinaldehyde receptor later gained K296 and became covalently light-sensitive. pitt A 2025 preprint reassigns some placopsins to melatonin-receptor-like GPCRs, so the earliest steps remain debated. researchgate The thematic point stands: the hormone of night and the receptor that announces day may share an ancestor.

3. How Old Genes Built the Mammalian Placenta

The placenta is the defining eutherian organ. It is transient yet vital, serving as fetal lung, gut, kidney, endocrine gland and immune shield; Burton and Fowden (Phil Trans R Soc B 2015) note that “it has been estimated that the placenta consumes 40% of the oxygen supplied to the feto-placental unit.” Retroviruses have infected vertebrates “for over 450 million years,” and Chuong (PLoS Biology 2018) notes that endogenous retroviruses (ERVs) are found throughout vertebrate genomes, “constituting over 8% of the human genome.” Notably, “there is an apparent propensity for ERVs to acquire new roles in the placenta” (Chuong, PLoS Biology 2018). nih

Syncytins: viral fusion genes, captured repeatedly

The syncytiotrophoblast, a fused cell sheet, handles exchange and blocks maternal immune cells. It is built by syncytins, the envelope (env) genes of ancient retroviruses. nih +3

Syncytin-1 (ERVW-1, HERV-W) is hominoid-specific; its receptor is ASCT2 (SLC1A5). wikidata nih
Syncytin-2 (ERVFRD-1) is shared across simians; its receptor is MFSD2A, and it has an immunosuppressive domain. nih
Syncytin-A/B belong to Muridae. Knockouts fail to fuse the syncytiotrophoblast, impairing “feto-maternal exchanges and embryo development and survival.” pnas
Syncytin-Car1 (Carnivora) was “the oldest syncytin gene identified to date” when described. pnas Others include syncytin-Ory1 (rabbit), syncytin-Rum1 (ruminants), syncytin-Opo1 (marsupials), a tenrec syncytin, and Mab-Env1 in the placental Mabuya lizard. wikidata +3

Lavialle et al. (Phil Trans R Soc B 2013) write that syncytins “have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution.” They were “acquired ‘by chance’ and yet still ‘necessary’.” The authors propose that a founding env capture was later “replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.” nih In the Carnivora paper, “all six syncytins are unrelated and correspond to independent captures in separate mammalian lineages.” pnas

Suppressyn: a viral brake

Suppressyn (ERVH48-1, 21q22.3) is a truncated HERV-H envelope protein. nih doi It was the first host-encoded mammalian protein shown to inhibit cell–cell fusion (Sugimoto et al., Scientific Reports 2013). nature It binds ASCT2 and restrains syncytin-1, and its expression is “largely limited to the human placenta.” nih Wikipedia Increased dosage in trisomy 21 is associated with the fusion defects of Down syndrome placentas. nature Both the accelerator and the brake are domesticated viral genes.

PEG10 and PEG11/RTL1

These are paternally expressed imprinted genes derived from a Ty3/Gypsy (sushi-ichi-related) retrotransposon that keep gag/pol-like domains. researchgate nih

Peg10. Knockout mice “showed early embryonic lethality owing to defects in the placenta,” lacking the labyrinth and spongiotrophoblast layers (Ono et al., Nature Genetics 2006). frontiersin nature
Peg11/Rtl1. It maintains fetal capillaries in mid-to-late gestation (Sekita et al., Nature Genetics 2008). frontiersin In humans its dysregulation underlies Kagami–Ogata and Temple syndromes. doi
PEG10 is therian-wide; PEG11/RTL1 is eutherian-only. wiley Kaneko-Ishino and Ishino (Biomolecules 2023) note that “Eutherians have 11 retrotransposon Gag-like (RTL)/sushi-ichi retrotransposon homolog (SIRH) genes,” of which “10 out of the 11… have been found to have essential and/or important functions.”

Rewiring the uterus

In placental mammals, endometrial stromal cells decidualize in response to progesterone and cAMP.

Lynch et al. (Nature Genetics 2011) found that “1,532 genes were recruited into endometrial expression in placental mammals.” Of these, “Thirteen percent… are located within 200 kb of a MER20 transposable element,” and MER20 elements “regulate endometrial-specific gene expression response to progesterone and cAMP.” MER20 “contributed to the origin of a novel gene regulatory network dedicated to pregnancy.” wordpress +2
Lynch et al. (Cell Reports 2015) found that “thousands of cis-regulatory elements that mediate decidualization and cell-type identity in decidualized stromal cells are derived from ancient mammalian transposable elements.” Lynch summarized: “Transposable elements appear to have brought this information, allowing old genes to be expressed in a new location, the uterus, during pregnancy,” and added that “immune suppression genes stand out.” nih +2
Decidual prolactin. Human decidual prolactin uses a promoter about 5.8 kb upstream of the pituitary promoter. It derives from the LTR element MER39 together with a MER20 enhancer, and it evolved by “a multistep process that took millions of years” (Emera and Wagner, PNAS 2012). nih +2 Mice use MER77 and elephants use L1-2_LA (Emera et al., MBE 2012): convergence by independent transposon recruitment. oup
ERV enhancers. The mouse ERV RLTR13D5 supplies hundreds of trophoblast enhancers bound by Cdx2, Eomes and Elf5 (Chuong et al., Nature Genetics 2013), implicating “ERV enhancer co-option as a mechanism underlying the extensive evolutionary diversification of placental development.” nature

4. Night and Day in the Qur’an: Signs for People of Understanding

These verses address those who reason (ya’qilun), reflect (yatafakkarun), know (ya’lamun), listen (yasma’un), are God-conscious (yattaqun), believe (yu’minun), and have understanding (ulu’l-albab) or vision (ulu’l-absar). The Arabic follows the Uthmani text of quran.com/tanzil.net. English is Sahih International unless marked. Sher Ali (Ahmadiyya) is given where verified; Ahmadiyya numbering is usually one higher because it counts the Basmalah.

The “alternation” verses

2:164 — إِنَّ فِى خَلْقِ ٱلسَّمَٰوَٰتِ وَٱلْأَرْضِ وَٱخْتِلَٰفِ ٱلَّيْلِ وَٱلنَّهَارِ وَٱلْفُلْكِ ٱلَّتِى تَجْرِى فِى ٱلْبَحْرِ بِمَا يَنفَعُ ٱلنَّاسَ وَمَآ أَنزَلَ ٱللَّهُ مِنَ ٱلسَّمَآءِ مِن مَّآءٍ فَأَحْيَا بِهِ ٱلْأَرْضَ بَعْدَ مَوْتِهَا وَبَثَّ فِيهَا مِن كُلِّ دَآبَّةٍ وَتَصْرِيفِ ٱلرِّيَٰحِ وَٱلسَّحَابِ ٱلْمُسَخَّرِ بَيْنَ ٱلسَّمَآءِ وَٱلْأَرْضِ لَءَايَٰتٍ لِّقَوْمٍ يَعْقِلُونَ “Indeed, in the creation of the heavens and the earth, and the alternation of the night and the day, … are signs for a people who use reason.” islamqa

3:190–191 — إِنَّ فِى خَلْقِ ٱلسَّمَٰوَٰتِ وَٱلْأَرْضِ وَٱخْتِلَٰفِ ٱلَّيْلِ وَٱلنَّهَارِ لَءَايَٰتٍ لِّأُو۟لِى ٱلْأَلْبَٰبِ ۝ ٱلَّذِينَ يَذْكُرُونَ ٱللَّهَ قِيَٰمًا وَقُعُودًا وَعَلَىٰ جُنُوبِهِمْ وَيَتَفَكَّرُونَ فِى خَلْقِ ٱلسَّمَٰوَٰتِ وَٱلْأَرْضِ رَبَّنَا مَا خَلَقْتَ هَٰذَا بَٰطِلًا سُبْحَٰنَكَ فَقِنَا عَذَابَ ٱلنَّارِ Sher Ali (3:191–192): “In the creation of the heavens and the earth and in the alternation of the night and the day there are indeed Signs for men of understanding; Those who remember Allah while standing, sitting, and lying on their sides, and ponder over the creation of the heavens and the earth: ‘Our Lord, Thou hast not created this in vain; nay, Holy art Thou; save us, then, from the punishment of the Fire.’” alislam alislam

10:6 — إِنَّ فِى ٱخْتِلَٰفِ ٱلَّيْلِ وَٱلنَّهَارِ وَمَا خَلَقَ ٱللَّهُ فِى ٱلسَّمَٰوَٰتِ وَٱلْأَرْضِ لَءَايَٰتٍ لِّقَوْمٍ يَتَّقُونَ “Indeed, in the alternation of the night and the day and [in] what Allah has created in the heavens and the earth are signs for a people who fear Allah.” surahquran surahquran

23:80 — وَهُوَ ٱلَّذِى يُحْىِۦ وَيُمِيتُ وَلَهُ ٱخْتِلَٰفُ ٱلَّيْلِ وَٱلنَّهَارِ ۚ أَفَلَا تَعْقِلُونَ “And it is He who gives life and causes death, and His is the alternation of the night and the day. Then will you not reason?”

45:5 — وَٱخْتِلَٰفِ ٱلَّيْلِ وَٱلنَّهَارِ وَمَآ أَنزَلَ ٱللَّهُ مِنَ ٱلسَّمَآءِ مِن رِّزْقٍ فَأَحْيَا بِهِ ٱلْأَرْضَ بَعْدَ مَوْتِهَا وَتَصْرِيفِ ٱلرِّيَٰحِ ءَايَٰتٌ لِّقَوْمٍ يَعْقِلُونَ “And [in] the alternation of night and day and [in] what Allah sends down from the sky of provision and gives life thereby to the earth after its lifelessness and [in His] directing of the winds are signs for a people who reason.”

Night for rest, day for sight and livelihood

10:67 — هُوَ ٱلَّذِى جَعَلَ لَكُمُ ٱلَّيْلَ لِتَسْكُنُوا۟ فِيهِ وَٱلنَّهَارَ مُبْصِرًا ۚ إِنَّ فِى ذَٰلِكَ لَءَايَٰتٍ لِّقَوْمٍ يَسْمَعُونَ “It is He who made for you the night to rest therein and the day, giving sight. Indeed in that are signs for a people who listen.”

25:47 — وَهُوَ ٱلَّذِى جَعَلَ لَكُمُ ٱلَّيْلَ لِبَاسًا وَٱلنَّوْمَ سُبَاتًا وَجَعَلَ ٱلنَّهَارَ نُشُورًا “And it is He who has made the night for you as clothing and sleep [a means for] rest and has made the day a resurrection.”

27:86 — أَلَمْ يَرَوْا۟ أَنَّا جَعَلْنَا ٱلَّيْلَ لِيَسْكُنُوا۟ فِيهِ وَٱلنَّهَارَ مُبْصِرًا ۚ إِنَّ فِى ذَٰلِكَ لَءَايَٰتٍ لِّقَوْمٍ يُؤْمِنُونَ “Do they not see that We made the night that they may rest therein and the day giving sight? Indeed in that are signs for a people who believe.”

28:71–73 — قُلْ أَرَءَيْتُمْ إِن جَعَلَ ٱللَّهُ عَلَيْكُمُ ٱلَّيْلَ سَرْمَدًا إِلَىٰ يَوْمِ ٱلْقِيَٰمَةِ مَنْ إِلَٰهٌ غَيْرُ ٱللَّهِ يَأْتِيكُم بِضِيَآءٍ ۖ أَفَلَا تَسْمَعُونَ ۝ قُلْ أَرَءَيْتُمْ إِن جَعَلَ ٱللَّهُ عَلَيْكُمُ ٱلنَّهَارَ سَرْمَدًا إِلَىٰ يَوْمِ ٱلْقِيَٰمَةِ مَنْ إِلَٰهٌ غَيْرُ ٱللَّهِ يَأْتِيكُم بِلَيْلٍ تَسْكُنُونَ فِيهِ ۖ أَفَلَا تُبْصِرُونَ ۝ وَمِن رَّحْمَتِهِۦ جَعَلَ لَكُمُ ٱلَّيْلَ وَٱلنَّهَارَ لِتَسْكُنُوا۟ فِيهِ وَلِتَبْتَغُوا۟ مِن فَضْلِهِۦ وَلَعَلَّكُمْ تَشْكُرُونَ “Say, ‘Have you considered: if Allah should make for you the night continuous until the Day of Resurrection, what deity other than Allah could bring you light? Then will you not hear?’ Say, ‘Have you considered: if Allah should make for you the day continuous until the Day of Resurrection, what deity other than Allah could bring you a night in which you may rest? Then will you not see?’ And out of His mercy He made for you the night and the day that you may rest therein and [by day] seek from His bounty and [that] perhaps you will be grateful.”

30:23 — وَمِنْ ءَايَٰتِهِۦ مَنَامُكُم بِٱلَّيْلِ وَٱلنَّهَارِ وَٱبْتِغَآؤُكُم مِّن فَضْلِهِۦٓ ۚ إِنَّ فِى ذَٰلِكَ لَءَايَٰتٍ لِّقَوْمٍ يَسْمَعُونَ “And of His signs is your sleep by night and day and your seeking of His bounty. Indeed in that are signs for a people who listen.”

40:61 — ٱللَّهُ ٱلَّذِى جَعَلَ لَكُمُ ٱلَّيْلَ لِتَسْكُنُوا۟ فِيهِ وَٱلنَّهَارَ مُبْصِرًا ۚ إِنَّ ٱللَّهَ لَذُو فَضْلٍ عَلَى ٱلنَّاسِ وَلَٰكِنَّ أَكْثَرَ ٱلنَّاسِ لَا يَشْكُرُونَ “It is Allah who made for you the night that you may rest therein and the day giving sight. Indeed, Allah is full of bounty to the people, but most of the people are not grateful.”

78:10–11 — وَجَعَلْنَا ٱلَّيْلَ لِبَاسًا ۝ وَجَعَلْنَا ٱلنَّهَارَ مَعَاشًا “And [We] made the night as clothing, and made the day for livelihood.”

6:96 — فَالِقُ ٱلْإِصْبَاحِ وَجَعَلَ ٱلَّيْلَ سَكَنًا وَٱلشَّمْسَ وَٱلْقَمَرَ حُسْبَانًا ۚ ذَٰلِكَ تَقْدِيرُ ٱلْعَزِيزِ ٱلْعَلِيمِ “[He is] the cleaver of daybreak and has made the night for rest and the sun and moon for calculation. That is the determination of the Exalted in Might, the Knowing.”

Two signs, reckoning, subjection

10:5 — هُوَ ٱلَّذِى جَعَلَ ٱلشَّمْسَ ضِيَآءً وَٱلْقَمَرَ نُورًا وَقَدَّرَهُۥ مَنَازِلَ لِتَعْلَمُوا۟ عَدَدَ ٱلسِّنِينَ وَٱلْحِسَابَ ۚ مَا خَلَقَ ٱللَّهُ ذَٰلِكَ إِلَّا بِٱلْحَقِّ ۚ يُفَصِّلُ ٱلْءَايَٰتِ لِقَوْمٍ يَعْلَمُونَ “It is He who made the sun a shining light and the moon a derived light and determined for it phases – that you may know the number of years and account [of time]. Allah has not created this except in truth. He details the signs for a people who know.”

17:12 — وَجَعَلْنَا ٱلَّيْلَ وَٱلنَّهَارَ ءَايَتَيْنِ ۖ فَمَحَوْنَآ ءَايَةَ ٱلَّيْلِ وَجَعَلْنَآ ءَايَةَ ٱلنَّهَارِ مُبْصِرَةً لِّتَبْتَغُوا۟ فَضْلًا مِّن رَّبِّكُمْ وَلِتَعْلَمُوا۟ عَدَدَ ٱلسِّنِينَ وَٱلْحِسَابَ ۚ وَكُلَّ شَىْءٍ فَصَّلْنَٰهُ تَفْصِيلًا “And We have made the night and day two signs, and We erased the sign of the night and made the sign of the day visible that you may seek bounty from your Lord and may know the number of years and the account [of time]. And everything We have set out in detail.” mquran medium

14:33 — وَسَخَّرَ لَكُمُ ٱلشَّمْسَ وَٱلْقَمَرَ دَآئِبَيْنِ ۖ وَسَخَّرَ لَكُمُ ٱلَّيْلَ وَٱلنَّهَارَ “And He subjected for you the sun and the moon, continuous [in orbit], and subjected for you the night and the day.”

16:12 — وَسَخَّرَ لَكُمُ ٱلَّيْلَ وَٱلنَّهَارَ وَٱلشَّمْسَ وَٱلْقَمَرَ ۖ وَٱلنُّجُومُ مُسَخَّرَٰتٌۢ بِأَمْرِهِۦٓ ۗ إِنَّ فِى ذَٰلِكَ لَءَايَٰتٍ لِّقَوْمٍ يَعْقِلُونَ “And He has subjected for you the night and day and the sun and moon, and the stars are subjected by His command. Indeed in that are signs for a people who reason.” inoor

21:33 — وَهُوَ ٱلَّذِى خَلَقَ ٱلَّيْلَ وَٱلنَّهَارَ وَٱلشَّمْسَ وَٱلْقَمَرَ ۖ كُلٌّ فِى فَلَكٍ يَسْبَحُونَ “And it is He who created the night and the day and the sun and the moon; all [heavenly bodies] in an orbit are swimming.”

41:37 — وَمِنْ ءَايَٰتِهِ ٱلَّيْلُ وَٱلنَّهَارُ وَٱلشَّمْسُ وَٱلْقَمَرُ ۚ لَا تَسْجُدُوا۟ لِلشَّمْسِ وَلَا لِلْقَمَرِ وَٱسْجُدُوا۟ لِلَّهِ ٱلَّذِى خَلَقَهُنَّ إِن كُنتُمْ إِيَّاهُ تَعْبُدُونَ “And of His signs are the night and day and the sun and moon. Do not prostrate to the sun or to the moon, but prostrate to Allah, who created them, if it should be Him that you worship.”

73:20 (clause) — …وَٱللَّهُ يُقَدِّرُ ٱلَّيْلَ وَٱلنَّهَارَ… “…And Allah determines [the extent of] the night and the day…”

Entering, covering, wrapping, succession

3:27 — تُولِجُ ٱلَّيْلَ فِى ٱلنَّهَارِ وَتُولِجُ ٱلنَّهَارَ فِى ٱلَّيْلِ ۖ وَتُخْرِجُ ٱلْحَىَّ مِنَ ٱلْمَيِّتِ وَتُخْرِجُ ٱلْمَيِّتَ مِنَ ٱلْحَىِّ ۖ وَتَرْزُقُ مَن تَشَآءُ بِغَيْرِ حِسَابٍ “You cause the night to enter the day, and You cause the day to enter the night; and You bring the living out of the dead, and You bring the dead out of the living. And You give provision to whom You will without account.”

7:54 (clause) — يُغْشِى ٱلَّيْلَ ٱلنَّهَارَ يَطْلُبُهُۥ حَثِيثًا “He covers the night with the day, [another night] chasing it rapidly.”

13:3 — وَهُوَ ٱلَّذِى مَدَّ ٱلْأَرْضَ وَجَعَلَ فِيهَا رَوَٰسِىَ وَأَنْهَٰرًا ۖ وَمِن كُلِّ ٱلثَّمَرَٰتِ جَعَلَ فِيهَا زَوْجَيْنِ ٱثْنَيْنِ ۖ يُغْشِى ٱلَّيْلَ ٱلنَّهَارَ ۚ إِنَّ فِى ذَٰلِكَ لَءَايَٰتٍ لِّقَوْمٍ يَتَفَكَّرُونَ “And it is He who spread the earth and placed therein firmly set mountains and rivers; and from all of the fruits He made therein two mates; He causes the night to cover the day. Indeed in that are signs for a people who give thought.”

22:61 — ذَٰلِكَ بِأَنَّ ٱللَّهَ يُولِجُ ٱلَّيْلَ فِى ٱلنَّهَارِ وَيُولِجُ ٱلنَّهَارَ فِى ٱلَّيْلِ وَأَنَّ ٱللَّهَ سَمِيعٌۢ بَصِيرٌ “That is because Allah causes the night to enter the day and causes the day to enter the night and because Allah is Hearing and Seeing.”

24:44 — يُقَلِّبُ ٱللَّهُ ٱلَّيْلَ وَٱلنَّهَارَ ۚ إِنَّ فِى ذَٰلِكَ لَعِبْرَةً لِّأُو۟لِى ٱلْأَبْصَٰرِ “Allah alternates the night and the day. Indeed in that is a lesson for those who have vision.” (Sher Ali, 24:45, opens: “ALLAH alternates the night and the day.”) islamawakened surahquran

25:62 — وَهُوَ ٱلَّذِى جَعَلَ ٱلَّيْلَ وَٱلنَّهَارَ خِلْفَةً لِّمَنْ أَرَادَ أَن يَذَّكَّرَ أَوْ أَرَادَ شُكُورًا “And it is He who has made the night and the day in succession for whoever desires to remember or desires gratitude.” medium

31:29 — أَلَمْ تَرَ أَنَّ ٱللَّهَ يُولِجُ ٱلَّيْلَ فِى ٱلنَّهَارِ وَيُولِجُ ٱلنَّهَارَ فِى ٱلَّيْلِ وَسَخَّرَ ٱلشَّمْسَ وَٱلْقَمَرَ كُلٌّ يَجْرِىٓ إِلَىٰٓ أَجَلٍ مُّسَمًّى وَأَنَّ ٱللَّهَ بِمَا تَعْمَلُونَ خَبِيرٌ “Do you not see that Allah causes the night to enter the day and causes the day to enter the night and has subjected the sun and the moon, each running [its course] for a specified term, and that Allah, with whatever you do, is Acquainted?”

35:13 (opening) — يُولِجُ ٱلَّيْلَ فِى ٱلنَّهَارِ وَيُولِجُ ٱلنَّهَارَ فِى ٱلَّيْلِ وَسَخَّرَ ٱلشَّمْسَ وَٱلْقَمَرَ كُلٌّ يَجْرِى لِأَجَلٍ مُّسَمًّى ۚ ذَٰلِكُمُ ٱللَّهُ رَبُّكُمْ لَهُ ٱلْمُلْكُ “He causes the night to enter the day, and He causes the day to enter the night and has subjected the sun and the moon – each running [its course] for a specified term. That is Allah, your Lord; to Him belongs sovereignty.”

36:37–40 — وَءَايَةٌ لَّهُمُ ٱلَّيْلُ نَسْلَخُ مِنْهُ ٱلنَّهَارَ فَإِذَا هُم مُّظْلِمُونَ ۝ وَٱلشَّمْسُ تَجْرِى لِمُسْتَقَرٍّ لَّهَا ۚ ذَٰلِكَ تَقْدِيرُ ٱلْعَزِيزِ ٱلْعَلِيمِ ۝ وَٱلْقَمَرَ قَدَّرْنَٰهُ مَنَازِلَ حَتَّىٰ عَادَ كَٱلْعُرْجُونِ ٱلْقَدِيمِ ۝ لَا ٱلشَّمْسُ يَنۢبَغِى لَهَآ أَن تُدْرِكَ ٱلْقَمَرَ وَلَا ٱلَّيْلُ سَابِقُ ٱلنَّهَارِ ۚ وَكُلٌّ فِى فَلَكٍ يَسْبَحُونَ “And a sign for them is the night. We remove from it [the light of] day, so they are [left] in darkness. And the sun runs [on course] toward its stopping point. That is the determination of the Exalted in Might, the Knowing. And the moon – We have determined for it phases, until it returns [appearing] like the old date stalk. It is not allowable for the sun to reach the moon, nor does the night overtake the day, but each, in an orbit, is swimming.” quran

39:5 — خَلَقَ ٱلسَّمَٰوَٰتِ وَٱلْأَرْضَ بِٱلْحَقِّ ۖ يُكَوِّرُ ٱلَّيْلَ عَلَى ٱلنَّهَارِ وَيُكَوِّرُ ٱلنَّهَارَ عَلَى ٱلَّيْلِ ۖ وَسَخَّرَ ٱلشَّمْسَ وَٱلْقَمَرَ ۖ كُلٌّ يَجْرِى لِأَجَلٍ مُّسَمًّى ۗ أَلَا هُوَ ٱلْعَزِيزُ ٱلْغَفَّٰرُ “He created the heavens and earth in truth. He wraps the night over the day and wraps the day over the night and has subjected the sun and the moon, each running [its course] for a specified term. Wikipedia Unquestionably, He is the Exalted in Might, the Perpetual Forgiver.”

57:6 — يُولِجُ ٱلَّيْلَ فِى ٱلنَّهَارِ وَيُولِجُ ٱلنَّهَارَ فِى ٱلَّيْلِ ۚ وَهُوَ عَلِيمٌۢ بِذَاتِ ٱلصُّدُورِ “He causes the night to enter the day and causes the day to enter the night, and He is Knowing of that within the breasts.”

Oaths

91:3–4 — وَٱلنَّهَارِ إِذَا جَلَّىٰهَا ۝ وَٱلَّيْلِ إِذَا يَغْشَىٰهَا “And [by] the day when it displays it, and [by] the night when it covers it.” Wikipedia

92:1–2 — وَٱلَّيْلِ إِذَا يَغْشَىٰ ۝ وَٱلنَّهَارِ إِذَا تَجَلَّىٰ “By the night when it covers, and [by] the day when it appears.”

Themes and the circadian bridge

Signs for the intellect. These verses invoke ‘aql, fikr, ‘ilm, hearing and sight. Verses 3:190–191 join reflection to remembrance and end with a verdict on purpose: rabbana ma khalaqta hadha batilan.
Rhythm as mercy. Verses 28:71–73 pose a thought experiment any sleep physician knows: endless night or endless day would be unlivable. Chronobiology confirms that losing the light–dark cycle, as in shift work, polar winters or ICU lighting, disrupts sleep, metabolism, mood and immunity.
Night as libas and sakan. Night is “clothing” and “rest,” and sleep is subat, cessation. Darkness lets the SCN release pineal melatonin. Melanopsin, tuned near 480 nm, the blue of the daytime sky, tells the brain that it is day. nih
Measure (taqdir). Verses 6:96, 10:5, 36:38 and 73:20 stress that night and day are measured. Our near-24-hour clock must be reset by light every day, and it is reset through an opsin repurposed from an ancient GPCR.
Day and seeing. Verses 17:12, 10:67, 27:86 and 40:61 call the day mubsir, “giving sight.” Rods and cones see; melanopsin knows it is day.

5. A Growing Portfolio of Repurposed Genes: The Case for Guided Evolution

The portfolio

Opsins. A melatonin-receptor-like GPCR became a light receptor. Duplication then yielded rods, cones (with the primate L/M split restoring trichromacy), melanopsin and neuropsin. After the nocturnal bottleneck, mammalian light sensing was rebuilt around the opsins that remained.
Optogenetics. Algal phototaxis genes became human tools for controlling neurons and restoring sight. Here the repurposing was done by human ingenuity.
Placenta. Retroviral env genes became syncytins in six or more lineages; another env became suppressyn; a Gypsy retrotransposon became PEG10/PEG11; and MER20, MER39, MER77, L1-2_LA and RLTR13D5 became the switches of pregnancy.

The mainstream explanation

Exaptation and co-option. Gould and Vrba’s term describes traits recruited for new roles. Lavialle et al. call syncytins “exapted”: acquired “by chance” yet “necessary” because each capture conferred “a positive selective advantage.” nih
Supply and filter. The International Human Genome Sequencing Consortium (Nature 2001) could “recognize about 45% of the genome” as transposable elements, a vast supply of raw material. Most insertions are neutral or harmful and are silenced; the rare useful ones are kept. Placental tissue is hypomethylated, which may explain why co-options cluster there. nih nature
Convergence through constraint. Retroviral envelopes are, by nature, membrane-fusion machines, so the physics of fusion keeps calling on them.
“Random” is technical. A commentary in Shah’s guided-evolution series notes that “random” means mutations “arise without regard to whether they will be useful to the organism. It does not mean uncaused, and it does not mean unknown.” thequran Selection is non-random.

None of this needs to be rejected by a theist.

Zia H. Shah MD’s perspective

Dr. Shah accepts common descent and argues that the data, read with the Qur’anic doctrines of divine knowledge and measure, point to guided evolution.

“Placenta: What a Retrovirus Did, Humanity Cannot.” With all our biotechnology we cannot build a placenta, yet a captured virus did. thequran The placenta serves as the baby’s lungs, gut and kidneys, sets up an “immune truce” for a semi-foreign fetus, and secretes hormones. Shah offers the elephant, with a placenta of ~9–21 kg and a 22-month gestation, as an example of scale. thequran
“Placenta From A Retrovirus: Accident Or Guided Evolution?” The placenta is a textbook exaptation and therefore counts against separate special creation. Yet the “repeated, independent co-option of viral genes for the same essential function in lineage after lineage looks less like luck than like a landscape shaped toward that outcome.” thequran thequran Elsewhere he writes: “for anyone with theistic ideology such amazing creativity speaks of guided evolution rather than a blind process.” thequran
“Viral Architects of the Placenta” and “Viruses as Architects of Mammalian Evolution.” These extend the argument to regulatory networks, since ERV long terminal repeats (LTRs) act as promoters and enhancers. In Shah’s words: “our placenta is, in a sense, a collaborative organ built with viral as well as cellular genes.” thequran
The truthfulness argument. If God had created humans and chimpanzees separately yet placed identical viral scars in both, “He would be presenting a false history in DNA, which contradicts the Islamic concept of a truthful Creator.” thequran
“The Marvel of Placenta: A Clue to Guided Evolution and Afterlife.” Reading 75:36–40, Shah links ‘alaqah, “a clinging form,” to the implanted embryo and placenta. He reasons from first creation to resurrection: the One who brought us through a drop and a clinging placenta “has more than enough power to bring the dead to life.” thequran thequran
Qur’anic vocabulary of guidance. thequran The series cites 87:1–3 (khalaqa fa-sawwa, wa’lladhi qaddara fa-hada: “who created and proportioned, and who determined and guided”) and 20:50 (“gave everything its form, then guided it”). The law is taqdir, measure; the outcome is hidayah, guidance. It also cites 71:14 (“in stages”), 71:17 (“grow from the earth as a growth”), and the present-tense yusawwirukum of 3:6.
Mutation and foreknowledge. The 2026 commentaries on 3:5–6 treat disease alleles and adaptive alleles as “the same kind of event,” distinguished by context, “and context is precisely what an omniscient Creator sees and a blind process cannot.” They cite sickle-cell, CFTR, CCR5-Δ32 and GULO, and note that the mutation rate sits in a narrow window between rigidity and error catastrophe.

Assessment

What the evidence shows. Reuse sits at the center of two defining mammalian traits: our circadian light sense and placental pregnancy. The same solutions also recur independently, in type I versus type II rhodopsins, in six or more syncytin captures, and in three different transposons recruited for prolactin. pnas oup

What guided evolution adds is interpretation, not a testable rival mechanism. Shah’s framework “requires no ‘god of the gaps,’ no interventions detectable in the laboratory.” Its strengths are cumulative:

The laws come before the process. Retroviral envelopes happen to fuse membranes, retinal happens to absorb visible light, and transposons happen to carry hormone-response elements. Evolution uses such raw material; it does not explain why it exists.
Convergence suggests a structured landscape. The theist reads that structure as taqdir; the naturalist reads it as constraint. The data are the same and the frameworks differ.
Fit. Verses 3:191 and 28:73 point to rest fitted to night, sight to day, and womb to fetus. A process that turns parasites into midwives and hormone receptors into eyes is at least compatible with ma khalaqta hadha batilan.

The honest conclusion. Co-option does not refute naturalistic evolution and should not be presented as if it did. It does weaken the rhetorical claim that evolution is “blind” in any sense beyond the technical one. For readers who already accept a Creator on wider grounds, it supplies empirically grounded signs of guidance working through natural processes.

Thematic Epilogue: The Light That Was Repurposed

The story begins with a single green cell in a pond, swimming toward the morning. In its eyespot is a protein that opens when light falls on it. For hundreds of millions of years that gene did one humble thing: it told an alga where the sun was. Then three scientists noticed it. Today that gene, carried by a virus and lit by amber goggles, lets a blind man reach for the edge of a table he can partly see. Stockholm calls it a switch for nerve cells. The Qur’an might call it fadl, bounty sought by day.

Inside our eyes is a different protein, unrelated to the alga’s, that solves the same problem the same way: seven helices, one lysine, one molecule of vitamin A. It may descend from a receptor once tuned to the hormone of darkness. One member of its family lets us see the day. Another, melanopsin, lets the brain know it is day and tells the pineal gland when to release the night. When a patient asks why midnight screens keep him awake, the answer runs back through this lineage to the verse: We made the night as clothing, and the day for livelihood.

In the “three darknesses” of the womb (39:6), another repurposing is at work. A retrovirus that once invaded an ancestor’s germline now fuses the cells that shelter the child. A second viral gene holds the first in check. A retrotransposon’s remnant builds the placental labyrinth. Ancient jumping genes taught the uterus to answer progesterone with prolactin. What was a parasite became a protector; what was an infection became an intimacy.

Biology names this exaptation and explains it by selection acting on abundant raw material. Faith need deny neither. It asks only the Qur’an’s question about night and day: is this batil, in vain? The ulu’l-albab, standing, sitting and lying on their sides, look at the same evidence the materialist sees and answer: Rabbana ma khalaqta hadha batilan. Our Lord, You did not create this in vain.

The night enters the day and the day enters the night. Old genes enter new lives. In both, those who reflect may find the same signature: the measure of the Mighty, the Knowing.