Suboptimal design

{{bronze}}
[[File:Orthobraces - dental braces lower upper jaw.jpg|thumb|right|165px|There's a good chance that God gave you suboptimal teeth.<ref name=ungar>[https://www.sapiens.org/body/human-teeth-evolution/ Why Are Human Teeth So Messed Up? Many of us have had crooked, ill-fitting teeth at some point in our lives. The reason has a lot to do with what we eat.] by Peter Ungar (26 Jul 2017) ''Sapiens''.</ref>]]
{{Evolution}}
{{cquote|Anyone who thinks that our body is a marvel of mechanical engineering should get out a phone book and scan the listings of orthodontists, orthopedists, optometrists, and [[chiropractor]]s—to name a few specialties. Those doctors are making good livings treating our sundry flaws. Face it: our body has ''many'' features that could work ''much'' better. The sad fact is that evolution is no [[engineer]]. It's just a tinkerer.|||Lewis I. Held, Jr.<ref name=held>''Quirks of Human Anatomy: An Evo-Devo Look at the Human Body'' by Lewis I. Held, Jr. (2009) Cambridge University Press. ISBN 0521732336.</ref>{{rp|105}}}}
{{cquote|[[God]] made man in his own image.|||Genesis 9:6 (English Standard Version) — Oopsie!}}
In many [[organism]]s, examples of '''suboptimal design''' or '''jury-rigged design''' can be seen. The existence of suboptimal design is evidence for 
intelligent
 inelegant design. These features can be explained easily by [[evolution]], the "''blind watchmaker''",<ref>See ''The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design'' by Richard Dawkins. ISBN 0393315703.</ref> which can only act on what it's given to act upon, but not by [[creationism]], or [[intelligent design]] (ID) (except by the Theory of "[[Omphalos|God created it that way to test our faith]]"), which states that a designer [[God]] created all organisms with a clean slate. Suboptimal design is generally not discussed in evolution, but there is some examination of the nature of evolutionary constraints. Public defenders of evolutionary theory like to keep it prominent anyway, as an answer to intelligent design's [[organized complexity]] and [[irreducible complexity]]. It is significant to observe that a single example of a suboptimal or otherwise imperfect design instantaneously falsifies the idea that a master designer has created by its intervention all life specifically tailored to fit its particular niche. [[The Fall]] has to be offered as an explanation if ID is to be internally coherent for evidence suggesting an error in the design of life by an allegedly flawless architect, with creationists claiming such event ruined perfection in God's work, especially in the case of humans, bringing in the examples given below together with [[aging]] and ultimately [[death]].

Thus, suboptimal design [[Morton's fork|forces ID proponents to decide]] whether they want to be scientists and acknowledge that their argumentation does not work (i.e. their hypothesis is wrong and must be discarded), or [[Pseudoscience|pseudoscientists]] who invent excuses, making their [[hypothesis]] [[unfalsifiable]] (i.e. their hypothesis is [[Not even wrong|disconnected from reality]] and does not deserve any respect).

[[Evolutionary developmental biology]] ("evo-devo") was left out of the [[modern synthesis]] of evolution that developed from the 1930s-1940s. Since then [[genetic]] analysis has given powerful tools to evo-devo that complement those of the modern synthesis (e.g., [[paleontology]], [[natural selection]]). The complete framework enables verifiable explanations for suboptimal design in organisms, whereas creationists have no other explanation than [[goddidit]].

A common evo-devo explanation for suboptimal design is what Lewis Held calls "bislagiatt", an acronym for "but it seemed like a good idea at the time".<ref name=held/>{{rp|105}} It explains:<ref name=held/>{{rp|105}}
{{cquote|suboptimal functioning of a structure due to (1) its being used in a novel context (e.g., a bipedal vs. quadrupedal stance) and (2) the inability of evolution to fix it (e.g., due to prohibitive demands of genomic rewiring). Tantamount to a species getting stuck on a low peak in a rugged adaptive landscape."}}

Examples of suboptimal design include non-functioning organs, [[vestigial features]] in general, and roundabout wiring.

==Non-functioning organs==
===Alulas in flightless ratites===
[[File:Alula.png|thumb|200px|right|Location of the alula on a bird's wing]]
The alula is a small structure located at the joint between the hand-wing and arm-wing of [[birds]], and is used for landing.<ref name="alula_1"> Sang-Im Lee et al. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423427/ The Function of the Alula in Avian Flight]. NCBI. 7 May 2015.</ref>  As the adherents of ID argue that a master [[intelligent designer]] created all life for its unique purpose, without error, it is most curious that we should see so many superfluous traits in so many taxa. Few examples are better than that of an alula, the "bastard-wing" or mid-wing slot formed by the thumb-borne remex, seen in Rheiformes (Rheidae family, flightless birds from South America), the reason for which is most difficult to account for, under the ID model.

===Land-vertebrate side toes===
[[File:PSM_V52_D352_Various_nail_walkers_toes.png|thumb|200px|right|Comparison of some tetrapod toes]]
All but some of the earliest tetrapods (land vertebrates and aquatic relatives) have at most 5 digits on each limb; 5 digits is their inferred ancestral state. However, in many cases, some of these digits have become reduced or absent, with the reduced ones having no clear function. In walking limbs, these extra toes no longer reach the ground.

[[Horse]] evolution shows an excellent series of intermediates between ''Hyracotherium'', with its four front toes and three rear toes, and ''Equus'', with its single toe on each foot.<ref name=mchorse>[https://royalsocietypublishing.org/doi/10.1098/rspb.2017.1174 Mechanics of evolutionary digit reduction in fossil horses (Equidae)] by Brianna K. McHorse et al. (2017) ''Proceedings of the Royal Society B: Biological Sciences'' doi:0.1098/rspb.2017.1174.</ref> The intermediates have the central toe enlarged and the toes on each side reduced, until present-day equines have only splints on each side.<ref name=mchorse/> However, present-day horses are occasionally born with three toes on each foot!<ref>[http://theperfecthoof.blogspot.com/2014/11/horse-toes.html Horse Toes?] (November 30, 2014) ''The Perfect Hoof''.</ref>

Parallel to horses, most artiodactyls (even-toed ungulates) have had a similar side-toe reduction; the main toes are 3 and 4, with 2 and 5 reduced or absent. Likewise, several carnivores, among them domestic [[dog]]s and [[cat]]s, have shortened toes with claws (dewclaws).<ref>[https://animaldiversity.org/accounts/Artiodactyla/ Artiodactyla: even-toed ungulates] ''Animal Diversity Web''.</ref>

Pandas' thumbs have become non-opposable, but they have evolved a new pseudo-thumb from the bones of the wrist.<ref>[http://s-f-walker.org.uk/pubsebooks/pdfs/Gould_Stephen_Jay_The_Panda%27s_Thumb.pdf ''The Panda's Thumb''] by Stephen Jay Gould (1980) W. W. Norton & Co. ISBN 0393308197. pp. 19-26.</ref>

==Vestigial features==
{{main|Vestigial features}}

===Amniote gill bars===
The [[embryo]]s of amniotes ([[reptile]]s, birds, [[mammal]]s) go through a phase where they have gill bars (or {{wpl|Gill slits}}) and gill pouches, though not functional gills; the aortic arches are to supply blood to these would-be gills.<ref name=held/>{{rp|65-67}}

Characteristics of embryos and the relationship to evolution is a hotly contested issue by the creationists. {{wpl|Haeckel's embryos}} are a particularly favorite whipping boy, especially in textbook debates.

===Appendix in humans===
{{main|Appendix}}

===Developmental pathways===
One of the most striking patterns observed in amniote ontogeny is the presence of highly conserved developmental pathways across lineages, except for a few glaring exceptions. Take, for instance, digital reduction in the manus. The manus is the part of the body to which the distal portion of the forelimb attaches. It is called the hand in primates, the front hoof in terrestrial Ungulates, the front paw in many Carnivores, the front flipper in marine mammals, etc.. The manus also makes up the wing in birds, [[Fun:bat|bat]]s, and [[pterosaur]]s. Morse's Law models the stereotypical, symmetrical reduction of manual digits via the loss of digits I and digits V.<ref name=shapiro>[https://www.researchgate.net/publication/41433314_Limb_diversity_and_digit_reduction_in_reptilian_evolution Limb diversity and digit reduction in reptilian evolution] by Michael D. Shapiro et al. (2007) In: ''Fins into Limbs: Evolution, Development, and Transformation'', edited by Brian K. Hall, pp. 225-244. ISBN 0226313360.</ref> Certain lepidosaurs (scaled lizards) and theropod [[dinosaurs]] mark the only known exceptions to this conserved pattern, in that in these groups digit IV is lost after serving as the organizational axis for the development of the digital arch, while digit I is retained and digit V reduced as usual.<ref name=shapiro/> This produces a highly specialized asymmetrical postaxial reduction pattern in the manus.<ref name=shapiro/> Such a seemingly inexplicable anomaly is readily accommodated by [[evolutionary biology]], but it is a significant problem for the ID model. If lizards and dinosaurs were created by the same [[intelligent designer|designer]] at the same time, why should they display so bizarre a pattern of digital reduction in the manus vis-a-vis all other amniotes?

===Diastataxy===
[[File:Black-capped_Kingfisher.jpg|thumb|200px|right|Black-capped Kingfisher (''Halcyon pileata'')]]
'''Diastataxy''' refers to the peculiar condition observed in basal neornithine lineages (modern birds excluding ratites) in which the fifth secondary remex (flight feather) is missing, but the corresponding secondary covert is present — leaving a diastema (gap) between the fourth and sixth secondary remiges. How this is the work of a "[[intelligent designer|master designer]]", or reflective of "intelligent design" is not readily apparent. The ID standpoint becomes most farcical when confronted by the hummingbird ''Cyanophaia caeruleolavata'' (Aves: Trochilidae) which is eutaxic in one wing and diastataxic in another! The kingfisher ''Halcyon pileata'' (Aves: Alcedinidae) displays an intermediary morphology between the eutaxic and diastataxic condition into adult ontogeny and thus provides a similarly inexplicable "design" quirk. Perhaps more bizarre yet is the hodgepodge distribution of diastataxy throughout Aves. For instance, all Charadrii are diastataxic except ''Philohela'', why? Why was this one particular genus singled out for eutaxy? Within Rallidae (rails), all but eight species are diastataxic. In another two genera of rails, ''Creciscus'' and ''Sarothrura'', both eutaxic and diastataxic species exist. Again the question must be, why? Why the erratic distribution of diastataxy and eutaxy? It strains credulity to advance "intelligent design" as the explanation for any of these examples.<ref>[http://digitallibrary.amnh.org/bitstream/handle/2246/1891/B034a06.pdf;jsessionid=633F80ED3B7C82062C30030C295C3F85?sequence=1 Notes on ptilosis, with special reference to the feathering of the wing] by Waldron DeWitt Miller (1915) ''Bulletin of the American Museum of Natural History'' 34(6):129-140.</ref><ref group=note>Just "throwing things at the wall to see what works" might be a design philosophy, but it's questionable whether or not it can be called "intelligent". In any case, it's more reasonable to believe that there's no design at all.</ref>

===Endosymbiosis===
{{main|Endosymbiosis}}

===Flowers of asexually-reproducing plants===
{{main|Flowers of asexually-reproducing plants}}

===Nipples on men===
[[File:Human nipple.jpg|thumb|right|165px|The male nipple]]
Why do males of almost all mammalian species have nipples? Creationists would be at a complete loss to explain this entirely useless feature. Embryology and evolution do however have an explanation. Mammalian fetuses do not physically differentiate by sex until the male fetus starts producing testosterone. In humans, that is at about 6 weeks. For males, there is little to no disadvantage to having nipples, and hence insignificant evolutionary selection against them.<ref name=held/>{{rp|98-101}} For example, cancer of the nipple is rare and usually occurs after reproduction.<ref>[http://www.scientificamerican.com/article/why-do-men-have-nipples/ Why do men have nipples?] by Andrew M. Simons (September 17, 2003) ''Scientific American''.</ref> Additionally, 1 in 18 people are born with supernumerary nipples.<ref>[https://medlineplus.gov/ency/article/003110.htm Supernumerary nipples]. ''medlineplus.gov''. Retrieved 19 March 2017.</ref> However, this is not the case for ''all'' mammals; for instance, males in mice, rats, and horses lack nipples.<ref>"[https://biology.stackexchange.com/questions/34150/evolutionarily-why-do-male-rats-and-horses-lack-nipples Evolutionarily, why do male rats and horses lack nipples?]" ''Biology Stack Exchange''. Retrieved 23 January 2019.</ref>

===Plantaris muscle===
The plantaris muscle is an example of suboptimal design. In the human species, it is atrophied (if not absent altogether) and ends in the Achilles tendon without reaching the toes at all. It is believed to be absent altogether in about 7 to 20% of humans.<ref name=simpson>[https://www.ncbi.nlm.nih.gov/pubmed/1880370 The plantaris tendon graft: an ultrasound study] by S. L. Simpson et al. (1991) ''J. Hand Surg. Am.'' 16(4):708-11.</ref> It is frequently used as a graft because its absence is usually not noticed.<ref name=simpson/>{{efn|Injury to the plantaris muscle was formerly believed to be the source of the painful "tennis leg", but this has been proven false.<ref>[https://www.sciencedirect.com/topics/neuroscience/plantaris-muscle Lower Leg, Ankle, and Foot Rehabilitation] by Edward P. Mulligan (2012) In: ''Lower Leg, Ankle, and Foot Rehabilitation'', edited by James R. Andrews et al. Saunders, 4<sup>th</sup> ed. ISBN 9781437724110. pp. 426-463.</ref>}}

In contrast, in monkeys, it is a fully functional muscle that serves to flex all toes at once, and is thus useful for swinging from trees by the feet. Its existence in human beings makes no sense for an intelligent designer, but makes perfect sense if we share a [[Common descent|common ancestry]] with the monkeys; it lost its functionality when we stopped swinging from trees, so people who lacked it weren't at any disadvantage relative to those who had it, and thus, it gradually disappeared.

===Pseudocopulation===
Lizards that reproduce by parthenogenesis ("[[virgin birth]]"), like the hybrids of certain whiptail (''Cnemidophorus'') species, often practice "pseudocopulation", in which a "pseudomale" bites a "pseudofemale" in the neck, inducing egg release.<ref>[https://www.desertmuseum.org/books/nhsd_whiptails.php Whiptails (''Cnemidophorus'' spp.)] ''Arizona-Sonora Desert Museum''.</ref> But a parthenogenetic species ought not to need this egg-release stimulus; aphids do not pseudocopulate when reproducing parthenogenetically.<ref>[https://study.com/academy/lesson/aphids-reproduction-life-cycle.html Aphids: Reproduction & Life Cycle] by Bryan Cowing, ''Study.com''.</ref> So it is clearly a vestigial feature left over from sexually-reproducing ancestors.

The reason why these lizards engage in pseudocopulation is to stimulate their hormonal cycles into peaking, in order to ovulate. Otherwise, they are incapable of automatically ovulating like, say, domesticated chickens (''Gallus gallus domesticus'').<ref>[http://wtamu.edu/~cbaird/sq/2013/11/21/why-did-evolution-create-a-chicken-that-lays-so-many-unfertilized-eggs-when-that-is-so-wasteful/ Why did evolution create a chicken that lays so many unfertilized eggs when that is so wasteful?] by Christopher S. Baird (November 21, 2013) ''Science Questions with Surprising Answers''.</ref>

===Seed plants' tiny gametophytes===
[[File:Alternation of generations simpler.svg|thumb|right|165px|Alternation of generations]]
Land plants practice alternation of generations between a diploid sporophyte phase and a haploid gametophyte phase; these phases produce spores and gametes, respectively. The more primitive plants, like mosses, liverworts, and ferns, have prominent sporophyte and gametophyte phases, but seed plants are nearly all sporophyte, having only microscopic gametophytes with only a few cells. The female gametophytes live inside of the parent plant's female reproductive parts (female cone, pistil,…), while the male gametophytes are released inside of pollen grains from the parent plant's male reproductive parts (male cone, stamen,…). When a pollen grain arrives at a compatible female reproductive part, it sprouts a pollen tube that contains the sperm-cell nuclei. This tube grows inside that part toward an embedded female gametophyte, where it fertilizes an egg cell.<ref>[https://www.ncbi.nlm.nih.gov/books/NBK9980/ Plant Life Cycles] by Scott F. Gilbert (2000) ''Developmental Biology'' Sinauer Associates, 6<sup>th</sup> edition. ISBN 0878932437.</ref>

This is clearly convergence toward the usual [[animal]] state of affairs of being all diploid except for the gametes; the tiny gametophytes are essentially vestigial, and could easily be done without.

===Vestigial carotids===
In the ''Bucorvus'' genus of birds (ground hornbills, the only extant genus of family Bucorvidae) and the ''Phaenicophaeus'' genus (ex-''Rhopodytes'' genus) of cuckoos, both of the common carotid arteries are vestigial, being present as only fibrous cords.<ref>[http://peabody.yale.edu/sites/default/files/documents/scientific-publications/ypmB39_1972.pdf A  Comparative  Study  of  the  Egg  White  Proteins  of  Non-Passerine  Birds] by Charles G. Sibley & Jon E. Ahlquist (1972) ''Peabody Museum of Natural History Bulletin'' 39(1).</ref>{{rp|23-24}} Their vascular function has been assumed by other vessels. The question therefore becomes, why should they be present at all? After all, if ''Bucorvus'' and ''Rhopodytes'' were designed in six literal days of creation and did not evolve, it follows that the "Master Designer" would have simply designed them with the appropriate vessels carrying out the vascular function of the carotids. Why waste resources on incorporating vestigial carotids into the "design"?

===Wings on ground-dwelling beetles===
[[File:Eleodesspp.jpg|thumb|200px|right|A species of ''Eleodes'', showing the fused elytra on its abdomen.]]
Flight is one of the main characteristics of [[insect]]s. However, many beetles (order Coleoptera) do not fly, such as some darkling beetles (family Tenebrionidae),<ref>[http://www.sfzoo.org/animals/invertebrates/darklingbeetle.htm Darkling Beetle, ''Eleodes''] ''San Francisco Zoo & Gardens''</ref> the Kauai flightless stag beetle (''Apterocyclus honoluluensis''),<ref>[http://www.bio-nica.info/Biblioteca/AnonimoApterocyclusHonoluluensis.pdf Kauai Flightless Stag Beetle ''Apterocyclus honoluluensis'', Coleoptera: Lucanidae] ''Bio-Nica''.</ref> and so on. And yet, they have wings. Not only do the beetles live &mdash; egg, larva, pupa, and adult &mdash; entirely on the ground, and so don't need wings; not only are their wings rather reduced, and so probably couldn't get the critter off the ground even if it wanted to go; no, the real wonder is that the wing covers (elytra) &mdash; which are themselves vestigial wings &mdash; are fused together, so that the wings themselves '''cannot''' be used!

===Yolk sac in mammals===
Humans and other mammals make a yolk sac (also known as an amnion) during the [[embryo]]nic phase of gestation despite making neither a shell-bearing egg nor a yolk (monotremes excepted). Why has the amnion persisted in mammalian development? Because it has taken up other roles during development. It is a source of blood stem cells and it functions as a resting location for primordial germ cells as they migrate.<ref name=held/>{{rp|128-129}} The persistence of the yolk sac can be a source of disease, causing {{wpl|Meckel's diverticulum||.}}<ref name=held/>{{rp|112-113}}

==Roundabout wiring==
===Aquatic air breathing===
[[File:Blow of a blue whale in the Arctic sea.jpg|thumb|right|165px|A blue whale (''Balaenoptera musculus'') exhaling in the Arctic Ocean]]
Many animals that live all or most of their life underwater still have to breathe air. These include the cetaceans (whales and [[dolphin]]s), sirenians (dugongs and manatees), pinnipeds (seals),<ref>[http://jeb.biologists.org/content/220/10/1761 Respiratory function and mechanics in pinnipeds and cetaceans] by Andreas Fahlman et al. (2017) ''Journal of Experimental Biology'' 220:1761-1773. doi:10.1242/jeb.126870.</ref> sea [[snake]]s (subfamily Hydrophiinae)<ref>[https://www.sciencedirect.com/science/article/pii/0034568774900024 Aquatic respiration in the sea snake'' Pelamis Platurus''] by Jeffrey B.Graham (1974) ''Respiration Physiology'' 21(1):1-7.</ref> and some large turtles.<ref>[https://www.jstor.org/stable/1444761?seq=1#page_scan_tab_contents Respiratory Physiology of Diving in the Sea Turtle] by Peter L. Lutz & Timothy B. Bentley (1985) ''Copeia'' 3:671-679.</ref> Some extinct groups of fully aquatic reptiles, such as the ichthyosaurs, mosasaurs, placodonts and plesiosaurs, also had to surface to breathe.<ref>"Locomotion and Respiration in Aquatic Air-Breathing Vertebrates" by Richard Cowen, In: ''Evolutionary Paleobiology'', edited by David Jablonski et al. University of Chicago Press. ISBN 0226389111. p. 337-354. Draft version: [http://mygeologypage.ucdavis.edu/cowen/ichthyosaur.html Locomotion and Respiration in Marine Air-Breathing Vertebrates]</ref>

These animals do not usually drown, since they do not inhale underwater, but they can suffocate if they don't get to the surface in time. This problem is marked because most aquatic air-breathers are viviparous or ovoviviparous, meaning that they give birth to live young which are born underwater. Taking the first breath is triggered by the touch of air on the skin; post mortems of dead calves sometimes show that they never got to the surface to take that first breath.<ref>[https://web.archive.org/web/20140530173340/https://www.scientificamerican.com/article/how-do-whales-and-dolphin/ How do Whales and Dolphins Sleep Without Drowning?] by Bruce Hecker (Feb 2, 1998)''Scientific American'' (archived from May 30, 2014).</ref>

Since this is an obvious problem, why not have gills or some other method of exchanging gases (extracting oxygen and removing CO<sub>2</sub>) with the water? Evolution can explain that these animals evolved from terrestrial animals which had no gills, and these gills haven't been able to re-evolve, but intelligent design offers no solution. It's not like the intelligent designer couldn't include both gills ''and'' lungs, especially in newborn animals, if it saw fit, since some animals like [[lungfish]] have both and salamanders have functional gills in the early stages of their development. In fact, it is unclear why these animals, especially those like sea snakes and ichthyosaurs with oxygen consumption similar to [[shark]]s and other [[fish]], should have to breathe air ''at all''.

===Biochemical pathways===
In 2004, Edward J. Behrman, George A. Marzluf, and Ronald Bentley published a paper titled, "Evidence from Biochemical Pathways in Favor of Unfinished Evolution rather than Intelligent Design".<ref name=behrman>[https://www.researchgate.net/publication/231266371_Evidence_from_Biochemical_Pathways_in_Favor_of_Unfinished_Evolution_rather_than_Intelligent_Design Evidence from Biochemical Pathways in Favor of Unfinished Evolution rather than Intelligent Design]." Behrman EJ, Marzluf GA, Bentley R (2004). ''Journal of Chemical Education.'' 81(7):1051-1052.</ref> The authors began by commenting:
{{cquote|In teaching metabolic pathways, every instructor emphasizes the chemical logic of the transformations wherever possible. In cases such as those to be described here, the lecturer is reduced to impotent [[Handwave|hand-waving]].}}

The examples listed are:<ref name=behrman/>
[[File:DNA replication en.svg|thumb|right|Schematic of DNA replication showing an Okazaki fragment]]
# Unnecessary transformation of a carbon atom from "left-handed" (S) to "right-handed" (R) chirality in the propionyl CoA→succinyl CoA pathway.
# The pathways for several compounds begin by converting (S)-reticuline to (R)-reticuline. It would be simpler to just use S-reticuline.
# Different organisms using different pathways for producing the same compound (the validity of this example might depend on what substrates are available)
# During the biosynthesis of the [[amino acid]] tryptophan ([https://web.archive.org/web/20090309152105/http://www.gwu.edu/~mpb/shikimate3.htm link to pathway]), a 3-carbon fragment is removed (glyceraldehyde 3-phosphate), and in the next step, a 3-carbon fragment (serine) is added back (actually, in this example, it seems that adding serine is probably a more direct way of getting the "backbone" part of the amino acid &mdash; it would take 3 steps to convert the glyceraldehyde 3-phosphate chain (-CHOH-CHOH-CHOPO<sub>3</sub>) into the amino acid carbon chain (CHH-CHNH<sub>3</sub>-COO).
# {{wpl|Okazaki fragments||.}} When [[DNA]] strands are separated and being replicated, the "leading strand" is continuously copied by a 5'→3' DNA polymerase. The "lagging strand" is unwound 3'→5', but because replication proceeds in the 5'→3' direction on the DNA strand, the lagging strand must be synthesized in short bits that are then pieced together.  It is pointed out that it would be simpler and more logical just to use a 3'-5' DNA polymerase on the lagging strand, but this is not what biology does.
# Unnecessary RNA editing. A pre-RNA for an ion channel [[protein]] has a particular codon, CAG, that codes for glutamine. However, if the protein that is produced from the RNA contains that glutamine, the mouse dies. In healthy mice, another protein edits the pre-RNA and changes CAG to CIG, which is equivalent to CGG and which produces arginine, the correct amino acid. It would be much simpler for the pre-RNA to just code for CGG to start with, and dispense the editing step. Indeed, scientists have made this change in the lab, and the resulting mice are normal and no longer need the editing step. This appears to be another example of unnecessary [[irreducible complexity]].

===Cellulose===
[[File:Types_of_Cellulase2.png|thumb|200px|right|The three types of reaction catalyzed by cellulases]]
'''Cellulose''' is a polysaccharide and is the principal component of the cell walls of [[plant]] [[cells]]. Cellulose is a polymer of glucose, the principal [[metabolism|metabolic]] substrate in respiration.

Coleridge's fabled ancient mariner might have lamented, were he of biologist leanings, "cellulose, cellulose everywhere and not a polysaccharide to  digest." Cellulose is the principal carbohydrate found in plant cell walls, and is the most abundant macromolecule on Earth.<ref name=alberts/> It is highly resistant to tensile forces, owing to its arrangement in long parallel aggregates, much like cables.<ref name=alberts>[https://www.ncbi.nlm.nih.gov/books/NBK26928/ "The Plant Cell Wall"] In: ''Molecular Biology of the Cell'' by Bruce M. Alberts et al. (2002) Garland Science, 4<sup>th</sup> ed. ISBN 0815340729.</ref> Composed entirely of glucose monomers,<ref>[https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Modules_(Biological_Chemistry)/Carbohydrates/Polysaccharides/Cellulose Cellulose] (Last updated Mar 11, 2015) ''Chemistry: LibreTexts''.</ref> cellulose is rich in chemical energy and presents a tempting meal for any animal that can metabolize it. Inexplicably, there are no known vertebrates that can digest cellulose on their own. Those few that can are forced to enlist the aid of [[bacteria]] and protozoans in their intestines that synthesize cellulase, an [[enzyme]] which can break down the glycosidic bonds that hold cellulose together. The vertebrates that enlist these intestinal symbionts are ruminant mammals<ref>[https://web.archive.org/web/20110927050243/http://arbl.cvmbs.colostate.edu/hbooks/pathphys/digestion/herbivores/microbes.html Fermentation Microbiology and Ecology] by R. Bowen (November 3, 1998) ''Pathophysiology of the Digestive System'', Colorado State University (archived from September 27, 2011).</ref> (e.g., [[sheep]], [[goat]]s, cattle, [[horse]]s, koalas, bison, buffalo, deer, and antelope). Considering the fact that cellulose is among the most abundant organic materials on [[Earth]], one must wonder why the "master designer" incorporated so glaring a defect as inability to digest it, into his multitude of designs.

Among invertebrates, endogenous cellulase production was found among some termites, wood-eating cockroaches, a snail, and earthworms.<ref name=watanabe>[https://pdfs.semanticscholar.org/30e9/93b7e5e8073748cc3687fcb21f1d1c95e804.pdf Animal cellulases] by H. Watanabe and G. Tokuda (2001) ''Cell. Mol. Life Sci.'' 58:1167-1178.</ref> In some cases, invertebrate cellulase may be partly-symbiotic.<ref name=watanabe/>

===Contralateral nerve wiring===
The nervous system of all animals crosses the midline before reaching the brain, thus the left side of one's brain controls the right side one's body and vice versa. This has been found to be true in vertebrates as well as invertebrates such as insects, nematodes, and flatworms. Two possible hypotheses might explain this roundabout wiring:<ref name=held/>{{rp|33-37}}
#Primitive ancient animals ({{wpl|Urbilaterians}}) may have used the criss-crossing of the nervous system to cause a reflex effect in response to predators, thus causing a muscular contraction on the opposite side of the stimulus and turning the body away from the predator.
#The criss-crossing may have evolved in response to undulatory motion, thus coordinating sinusoidal swimming.

===Descendant testes in humans and other primates===
In [[humans]] and related primates, males develop [[Testicles|testes]] deep in the abdomen. The testes then descend to the scrotum. In order to accomplish this, a hole must form in the peritoneum (lining of the abdomen) through which the testes pass on their way. This hole is sealed, but not well. This faulty seal is unsuited for bearing the weight of the organs a human puts upon it, and frequently tears in later life, resulting in the most common type of hernia, an inguinal hernia,<ref>[https://www.verywellhealth.com/inguinal-hernias-diagnosis-and-surgical-treatment-3157229 Inguinal Hernias — Diagnosis and Surgical Treatment] by Jennifer Whitlock (December 31, 2018) ''Verywell Health''.</ref> as well as risk of sterility from untreated cryptorchidism.<ref name=held/>{{rp|112-113}} 

====Evolutionary history of descendant testes====
The formation of the testes in the abdomen is a common situation in vertebrates. In cold-blooded vertebrates, it makes sense. The testes work most efficiently if they can be kept at a constant temperature, and the closest thing to constant in a cold-blooded creature is towards the center of the body.

When warm-blooded traits began to evolve, the body temperature of mammals began to exceed the safe functional range of the testes. The testes had to be cooled. Different lines of descent in the mammals have solved this problem in different ways. Some species develop elaborate cooling systems around the testes. Others, such as ourselves and our primate ancestors, move the testes closer to the skin so that they may easily radiate excess heat.

Why form the testes in the abdomen and move them rather than just form them in the scrotum? Because evolutionary change is always easiest to accomplish by tacking steps onto the end of a process rather than modifying existing steps that work. It's just simpler to produce this kind of development. It's easy to see how each step closer to the surface was an incremental improvement in the situation, so this poses no challenge to evolution.

Why isn't the seal on the peritoneum better? Because for most of our evolutionary history, it didn't need to be. Our quadruped ancestors put no great weight on the seal, and so the seal had no tendency to rupture.  When we started to walk upright, the weight of our internal organs was no longer borne by the front of our belly and by the supports hanging from our spines, but rather by the lower portion of our peritoneum. The seal that had been more than sufficient since we evolved into mammals suddenly became a design flaw.

There has been insufficient evolutionary pressure to produce a more effective arrangement, probably because most inguinal hernias occur late in life; most evolutionary pressure is focused on diseases that occur during reproductive ages and earlier. This is but one of several elements of our anatomy that shows insufficient adjustment from our quadruped ancestors. (Another being the aforementioned organ supports hanging from our spines, which are quite unsuited for life as a biped and are a major cause of lower back pain in later life.)

====Creationism and descendant testes====
Creationism has a much more difficult time explaining the descendant testes.

In general terms, creationists react to such obvious examples of bad design in various ways, none of which adequately explains the descendant testes.

* Creationists frequently claim that apparent examples of bad design are, actually, good design, if looked at in the proper light. There seems little possibility of finding a "good purpose" for this formative arrangement, and until they come up with one, this is just blowing smoke. By all appearances, this is bad design for which a superior design is patently obvious. Claiming it is anything else requires some support.

* Creationists may lay the blame for bad design on "degeneration" caused by [[The Fall]]. It would certainly be possible to posit that the testes were moved from a better location to the abdomen as a result of degeneration, but how to account for them moving back? Isn't this a positive change that would have to occur after their initial misplacement, such that creationists deny is possible? Degeneration of the peritoneum to allow the testes through is probably acceptable to creationists, but the seal, as poorly designed as it is, is still an improvement over no seal, and thus the creationists deny they are possible to form. (That degeneration runs contrary to natural selection, which most creationists claim to accept, is another issue.)

In the end, creationists simply have no effective explanation for the process by which our testes descend. The clearly poorly-executed design of the system, along with an obvious history of improvements to it, denies the foundation of most creationist anti-evolution arguments and the descent of the testes must be seen as evidence against creationism.

===Embryonic wasted developments===
During development, embryos form organs that are later destroyed or repurposed. Human embryos form a tail that later in development becomes the coccyx and sacrum, but in rare cases babies are born with a tail.<ref name=held/>{{rp|57-59}}

Land-dwelling vertebrates have gill slits during embryonic development. Ordinarily, all except the first slit on each side disappears, and the first slit becomes the ear canal.<ref name=held/>{{rp|65}} In some cases, the gill slits persist and become cervical or pharyngeal fistulae.<ref name=held/>{{rp|65}} The embryos also develop aortic arches that in fish would supply blood to the gills, but in land vertebrates are destroyed completely in later development.<ref name=held/>{{rp|67}}

===Endogenous retroviruses===
For the most part, ERVs are genomic fossils of ancient [[viruses]]. Some, however, still retain functionality and have to be kept under control by the immune system. Mice lacking immune components undergo reactivation of these sequences.<ref name=Carey_N_JunkDNA>Carey, N. "Junk DNA. A Journey Through the Dark Matter of the Genome". ''Columbia University Press''. 20 June 2017.</ref>{{rp|42}}

===Flounder eyes and mouths===
[[File:Bothus_lunatus.jpg|thumb|165px|right|As you can see from this photo of ''Bothus lunatus'', the mouth is still sideways, representing the ancestral condition when the fish swam upright like normal fish.]]
Flounders and other flatfish (halibut, etc.) spend most of their lives lying on the sandy bottom of the ocean. However, unlike skates and rays, flounders clearly have a "jury-rigged" solution to life on the ocean floor. When flounders are young, they swim upright like normal fish. However, as they get bigger, they begin to swim and lay on their sides. The problem with this is that one eye is facing the wrong way, into the sand. The solution? The eye actually pops out of its socket and migrates around to the <i>other side</i> of the face!<ref name=held/>{{rp|28}}

===Fruit fly penis===
During metamorphosis, the penis of fruit flies (''Drosophila'') pointlessly rotates 360° around the anus. An explanation for this is likely that a fruit fly ancestor's penis only rotated 180° and did so for the purposes of mating position, as is the case of some primitive flies (mosquitoes). When fruit fly ancestors ceased using that mating position, they then would have faced selection pressure to rotate the penis either 0° or 360°.<ref name=held/>{{rp|20}}<ref>Anatomie und Variabilität des Geschlechtsapparates von ''Drosophila melanogaster'' (Meigen) by R. Gleichauf (1936) ''Z. wiss. Zool. Abt.'' A 148:1-66.</ref><ref>[http://www.ijdb.ehu.es/web/paper.php?doi=10.1387/ijdb.041859am PVF1/PVR signaling and apoptosis promotes the rotation and dorsal closure of the ''Drosophila'' male terminalia] by Ana Macías et al. (2004) ''Int. J. Dev. Biol.'' 48:1087-1094. doi:10.1387/ijdb.041859am.</ref>

===Human childbirth===
[[Childbirth]] in humans (and formerly in [[Neanderthal]]s), particularly unaided by modern medicine, is dangerous because evolution has made babies' heads larger and larger within {{wpl|hominin}} subtribe due to selection pressure for greater intelligence. Hominins have also faced selection pressure for bipedal speed, and that has placed limits on female hip size. The baby's head must still pass through the birth canal and therefore through the mother's pelvis, and in doing so, the baby contorts itself and distorts its skull shape. The risks to the baby include permanent paralysis from ripping nerve roots at the shoulder, and the risk of death for both the mother and baby when the baby's head is too large to fit through the birth canal.<ref name=held/>{{rp|123-125}} If godddidit, He could have designed a safer way of giving birth by avoiding the pelvis entirely, such as with hyenas who give birth through their enlarged clitorises (pseudopenises).<ref name=held/>{{rp|108}}

===Humeral elevators in Aves===
{{More sources}}
[[File:Wing_Muscles,_color.svg|thumb|200px|right|A diagram of bird anatomy involved in flight, indicating muscles (shades of red) and bones (shades of yellow).]]
Essentially, the [[Bird|avian]] pectoral apparatus is wired backwards from that seen in the only other extant flying vertebrates, bats. Logically, the dorsal elevators such as the deltoids ought to be the principal muscles affecting elevation of the humerus, and indeed this is what we see in bats. In birds, however, a ventral muscle, ''Musculus supracoracoideus'', affects elevation of the wing via a deflected tendon of insertion. Thus a muscle which initially functioned as a humeral depressor, has undergone a complete reversal in function. Why didn't our alleged "[[intelligent designer|master designer]]" just wire things right from the outset, with the dorsal musculature elevating the wing? Why the convoluted (literally) system whereby a ventral muscle elevates the wing through a looped tendon of insertion?

===Land-vertebrate blood circulation===

This starts off in fish-like fashion and gets reorganized, with some aortic arches and other vessels dropping out.<ref name=hearts>[https://inside.ucumberlands.edu/academics/biology/faculty/kuss/courses/CirculatorySystem/ComparativeHearts.htm The Circulatory System: Comparative Look at Vertebrate Hearts] ''University of the Cumberlands''.</ref> Likewise, the heart starts off as a two-chambered, fish-like heart and becomes split into a three-chambered heart and sometimes further into a four-chambered heart with two separate blood paths.<ref name=hearts/> But why not start out with some intended final state if that is what is desired? Why build some extra blood vessels, only to throw them away? Why not make the heart start off as three- or four-chambered?

===Mammalian tidal respiration===
Mammals have a lung ventilation system that is tidal: we breathe in and out through the same tubing. Deoxygenated air is therefore mixed with the fresh, and some of it is re-breathed. 

[[File:BirdRespiration.svg|thumb|200px|right|Schematic of bird respiration]]
Birds, however, have a different system. It is 'through-flow': the air follows a circular path round the body to the lungs and out again, so that oxygen-rich incoming air is '''not''' mixed with the deoxygenated outgoing air. It has been calculated that the avian system is therefore 10 times more efficient than the mammalian one. That is, mammals &mdash; including us humans &mdash; have far less efficient lungs than birds.<ref>[http://fsc.fernbank.edu/Birding/respiration.htm Fernbank Science Center's Ornithology Web: Respiration]</ref>

What makes this doubly odd is that there are many mammals whose lifestyles mean efficient breathing is essential: long-distance runners like wolves and African hunting dogs, and sprinters like [[cheetah|cheetahs]]. And really oddly, the mammalian equivalent of birds, bats. What is it about the bat lifestyle (say, a pipistrelle), compared to the bird lifestyle (say, a nightjar), that means it deserves lungs so inefficient? And conversely, the avian system is found in hawks and albatrosses, pigeons and peregrines. Fair enough. But it's also used in kiwis, penguins, and ostriches. What on earth was the designer up to?!

Interestingly, in the case of bats, they have perhaps the most efficient respiratory system of any mammal.<ref>[http://jeb.biologists.org/content/57/2/317.short The Physiology and Energetics of Bat Flight] by Steven P. Thomas & Roderick A. Suthers, ''Journal of Experimental Biology'' 1972 57: 317-335.</ref> It means that bats can make a good go at a bird-like way of life. But it is good in spite of the aforementioned problem. It ''overcomes'' the tidal system's disadvantages. But there's the rub: if bats were designed from scratch, why include a disadvantage and use add-ons to fix it? Especially if there is a more efficient system (the bird one) available? If mammals were cars, they all would have one-litre four cylinder engines, regardless of use… and the racing cars — bats — would have had a turbocharger added.

===Organ fusion during development===
Several symmetric organs in vertebrates fuse together from separate parts along the midline of symmetry during development, including the heart, the palate, the sternum, the uterus, the urethra, and the face.<ref name=held/>{{rp|37}} Failure to fuse properly can cause medical problems, including cardia bifida, cleft sternum, duplex uterus, hypospadias, facial displasias, and cleft nose.<ref name=held/>{{rp|37}} A better design for these organs might have been to form them whole rather than in pieces.<ref name=held/>{{rp|37}} The evo-devo explanation for this type of development is that the organs form tubes via invagination of cell sheets, rather than the possibly safer formation via cavitation of solid cylinders.<ref name=held/>{{rp|37}} This is widespread across [[metazoa]]ns, and likely began with the ancient Urbilaterans.<ref name=held/>{{rp|38}} The fusion of the pancreas can sometimes lead to a ring-shaped pancreas that leads to strangulation of the duodenum.<ref name=held/>{{rp|112-113}}

===Reptile cardiopulmonary capability===
Reptiles display a marvelous example of a cardiorespiratory system which is incongruent with the idea that all taxa were designed without flaw by a master builder. Reptiles are theoretically capable of powering a high resting metabolic rate (equal to or exceeding the avian minimum of 40 kcal/kg<sup>0.75/day</sup>), but are in fact unable to meet the oxygenation requirements of such a resting metabolic rate.<ref name="ruben1995">Ruben, J. 1995. The evolution of endothermy in mammals and birds. ''Annual Review of Physiology'' 57: 69-95.</ref><ref name="thompson1997">Thompson, G. G. & Withers, P. C. 1997. Standard and maximal metabolic rates of goannas. ''Physiolocial Zoology'' 30: 611-634.</ref> Nevertheless, reptile lungs (especially those of crocodiles) are usually quite large. How can this discrepancy be? Simple: reptile lungs have a low surface area to volume ratio compared to say mammals (i.e. reptile lungs have less branching). They cannot power a high resting metabolic rate because the low blood-flow rate of the reptilian heart is combined with the simple structure of the reptilian lung (size notwithstanding), in which the surface area/volume ratio is itself minimal. Thus, we have yet another example of suboptimal design to contradict the ID model.<ref name="ruben1995"/><ref name="thompson1997"/>

===Urate oxidase===
An enzyme that oxidizes uric acid into 5-hydroxyisourate, finally yielding allantoin and CO<sub>2</sub>. Its gene became non-functional in early primate evolution,<ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC298506/ Urate oxidase: primary structure and evolutionary implications] by X. W. Wu et al. (1989) ''Proc. Natl. Acad. Sci. USA'' 86(23):9412–9416.</ref> so overeating animal-derived food can cause gout. This has been hypothesized as a beneficial [[mutation]], since increased plasma urate has protective [[antioxidant]] effects that lengthen the lifespan. But still, the protective effect shows up in the blood. Many other enzymes show tissue-specific regulation, so there is no known reason to render this auxiliary gene completely non-functional.

===Vertebrate eye===
{{main|Eye#Tell-tale signs of evolution|Eye}}

==Additional suboptimal designs in humans==
{{collist|2|
*Ankle and knee weakness predisposes humans to sprains as a result of bipedalism.<ref name=held/>{{rp|110-111}}
*Blood vessel routing in the leg can lead to clots.<ref name=held/>{{rp|110-111}}
*Having a single pacemaker in the heart increases the risk of heart attacks.<ref name=held/>{{rp|110-111}}
*Lung connection to the foregut can lead to choking.<ref name=held/>{{rp|110-111}}
*Ear muscles are useless.<ref name=held/>{{rp|110-111}}
*Mammalian inner ear hair cells that do not recover or regenerate – God must want to teach a sadistic lesson to metalheads!
*Muscles that cause goose bumps have no function.<ref name=held/>{{rp|110-111}}
*Nerve wiring: 1) left recurrent laryngeal nerve is excessively long 2) sciatic nerve is prone to entrapment syndromes.<ref name=held/>{{rp|110-111}}
*Oviduct is excessively long, sometimes leading to tubal pregnancies.<ref name=held/>{{rp|110-111}}
*The prostate circling the urethra can lead to age-related urination problems.<ref name=held/>{{rp|112-113}}
*The venous plexus near the rectum can cause hemorrhoids from a sedentary lifestyle.<ref name=held/>{{rp|112-113}}
*Poor sinus drainage leads to sinus infections.<ref name=held/>{{rp|112-113}}
*Spinal curvature leads to backaches and herniated discs.<ref name=held/>{{rp|112-113}}
*Tooth overcrowding can lead to impacted wisdom teeth.<ref name=ungar/><ref name=held/>{{rp|112-113}}
*The long umbilical cord can lead to strangulation during birth.<ref name=held/>{{rp|112-113}}
*The vas deferens is unnecessarily long.<ref name=held/>{{rp|112-113}}
}}

==A programmer's view==
[[File:Jim Kent.JPG|thumb|right|165px|Jim Kent in 2007]]
In 2003 {{wpl|Jim Kent}} {{lived|1960}}, at the time a biology graduate student (and later Director of the University of California Santa Cruz Genome Browser Project),<ref>[https://cbse.soe.ucsc.edu/people/kent Jim Kent home page]</ref> gave an interview to ''Salon'' on his views of the human genome from a computer science perspective, below is an excerpt:<ref>[https://www.salon.com/2003/10/21/genome_5/ How I decoded the human genome] by John Sundman (Tuesday, Oct 21, 2003 12:30 PM PDT) ''Salon''</ref>
{{cquote|Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of [[DNA]] as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code &mdash; not God’s most sublime handiwork, but some hack’s kludge riddled with countless generations of side effects, and "[[parasite]]s on parasites."<br /><br />

"It’s a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, [[cells]] are like processes… the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That’s why a lot of people say, 'The [[genome]] is [[Junk DNA|junk]].'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.}}

==See also==
*[[Laryngeal nerve]]
*[[List of mistakes made by God]]

==External links==
*[http://creationwiki.org/Suboptimal_design Response to this article on CreationWiki] - None of the previous "design flaws" we analyzed is refuted. They merely claim that Creationism does not mean optimal design in the natural world.
*[http://www.freewebs.com/oolon/SMOGGM.htm Some More Of God's Greatest Mistakes] &mdash; Gives many more examples with short summaries
*A 2004 paper: Behrman EJ, Marzluf GA, Bentley R (2004). "[http://jchemed.chem.wisc.edu/Journal/Issues/2004/Jul/abs1051.html Evidence from Biochemical Pathways in Favor of Unfinished Evolution rather than Intelligent Design]." ''Journal of Chemical Education.'' 81(7):1051-1052.
*[http://winace.andkon.com/designed_organisms/ Organisms That Look Designed] &mdash; A subtle (?) ''reductio ad absurdum'' for the whole Intelligent Design hypothesis.
*[http://whale.wheelock.edu/whalenet-stuff/sleeppage/ How do whales and dolphins sleep without drowning?] by Bruce Hecker, director of husbandry at the South Carolina Aquarium

==Notes==
{{reflist|group=note}}

==References==
{{reflist|2|80%}}

{{crebox}}

[[Category:Anatomy]]
[[Category:EvoWiki ports]]
[[Category:Evolution]]
[[Category:Biology]]
[[Category:Creationism]]
[[Category:Intelligent design creationism]]
[[Category:Suboptimal design| ]]

Categories: Anatomy, EvoWiki ports, Evolution, Biology, Creationism, Intelligent design creationism, Suboptimal design