his is a post that presents evidence to back up my claim that there is evidence of jury-rigged design in nature. The first part is mine, the rest is assembled from contributions of others. This is extremely long, but interesting (IMHO). I just sort of collected all the posts below mine and I don't have the others permission to post them. But, I would suspect they don't mind (or they wouldn't have posted it in the first place. In any case, I'd like to thank all the contributors to this almost Meritt-like gargantuan post. (Loren Petrich, Matt Wiener, Herb Huston, Paul Keck and Keith Doyle)

Many organisms show features of appallingly bad design. This is because evolution via natural selection cannot construct traits from scratch; new traits must be modifications of previously existing traits. This is called historical constraint. A few examples of bad design imposed by historical constraint:

In parthenogenetic lizards of the genus Cnemdophorus, only females exist. Fertility in these lizards is increased when another lizard engages in pseudomale behavior and attempts to copulate with the first lizard. These lizards evolved from a sexual species so this behaviour makes some sense. The hormones for reproduction were likely originally stimulated by sexual behaviour. Now, although they are parthenogenetic, simulated sexual behaviour increases fertility. Fake sex in a parthenogenetic species doesn't sound like good design to me.

In African locust, the nerve cells that connect to the wings originate in the abdomen, even though the wings are in the thorax. This strange "wiring" is the result of the abdomen nerves being co-opted for use in flight. A good designer would not have flight nerves travel down the ventral nerve cord past their target, then backtrack through the organism to where they are needed. Using more materials than necessary is not good design.

In human males, the urethra passes right through the prostate gland, a gland very prone to infection and subsequent enlargement. This blocks the urethra and is a very common medical problem in males. Putting a collapsible tube through an organ that is very likely to expand and block flow in this tube is not good design. Any moron with half a brain (or less) could design male "plumbing" better.

Perhaps one of the most famous examples of how evolution does not produced designed, but "jury-rigged" traits is the panda's thumb. If you count the digits on a panda's paw you will count six. Five curl around and the "thumb" is an opposable digit. The five fingers are made of the same bones our (humans and most other vertebrates) fingers are made of. The thumb is constructed by enlarging a few bones that form the wrist in other species. The muscles that operate it are "rerouted" muscles present in the hand of vertabrates (see S.J. Gould book "The Panda's Thumb" for an engaging discussion of this case). Again, this is not good design.

From: lip@s1.gov (Loren I. Petrich)
Subject: Vestigial Features: Contributions for a FAQ list

Since most of the examples that would probably be submitted will be animal-kingdom ones, I'd like to take a look outside.

Plants

Alternation of generations:

Many algae and "lower" plants, like mosses and ferns, have an alternation of generations between an asexual diploid phase and a sexual haploid phase. In ferns and similar plants, it is the diploid phase which is the most prominent; it reproduces by producing spores. The haploid plants are small ones that release egg and sperm cells; they need damp ground for the sperms to swim to the eggs in, thus limiting ferns' habitats. Looking at the "higher" plants, the gymnosperms and the angiosperms, we find that just about all of the plant is the diploid phase. The female haploid phases grow in the reproductive organs of the diploid phases; they are only a few cells in angiosperms. The male haploid phases are released as pollen; when they alight on the diploid phases' reproductive organs, they sprout a tube that attempts to find the female haploid phase. Haploid phases bigger than one cell are a vestigial feature here.

Flowers of self-pollinators:

Some flowering plants, like dandelions, are self-pollinating, and thus have no need of flowers to attract pollen carriers.

Vestigial flower parts:

Some non-flowering angiosperms, like the grasses, apparently have vestigial flower parts.

Cells

Mitochondria and chloroplasts in eukaryotic cells:

Eukaryotic cells (those with distinct nuclei) typically have rather complex internal structure. Most of this structure is generated from the cell's fluid matrix, but there are important exceptions. These are the mitochondria and the chloroplasts (as well as different-colored plastids). Mitochondria perform energy metabolism, combining electrons from food with oxygen (and hydrogen ions) to make water. Chloroplasts do photosynthesis. These organelles contain their own genes and their own DNA->RNA->protein synthesis systems. Why that should be necessary is not clear, given the other internal structures that do not need self-contained genetic systems, and also given the fact that many of the genes for proteins used in the mitochondria and chloroplasts reside in the nucleus.

The answer to this riddle is that they are descended from free-living cells, which, of course, would need their own genetic systems. This is evident by comparing sequences of macromolecules like Cytochrome C and ribosomal RNA, as well as by comparing details of internal structure.

The mitochondria turn out to be related to the Purple Bacteria, which photosynthesize by a simpler process (one photosystem instead of two) than oxygen-releasing photosynthesizers do, and which use sulfur or organic compounds instead of water as their starting point. The family tree of the Purple Bacteria includes many non-photosynthetic bacteria; these include many of the classical Gram-negative (from their response to a certain stain) ones like the root-nodule bacteria and Escherichia coli.

The chloroplasts turn out to be descendants of the cyanobacteria, or blue-green algae. Chloroplast capture by eukaryotic cells probably happened several times, producing the different lineages of eukaryotic algae. In some cases, a "chloroplast" turns out to have once been a eukaryotic alga, indicating that this process can be repeated.

The riddle of the mitochondrial and chloroplast proteins whose genes reside in the nucleus can be resolved by supposing that the genes were transferred there. There may have been selection pressure in favor of this transference if the nuclei copy genes with greater fidelity than the mitochondria or chloroplasts do.

Thus, the genetic systems of the mitochondria and chloroplasts are vestigial features dating back from a free-living existence.

Oxygen Metabolism:

There is a remarkable feature of oxygen metabolism all across Earth organisms. In most cases, it is either the last (for respiration) or the first (for photosynthesis) step in the various metabolic pathways. Furthermore, there is more variation in the molecules used for the final steps of respiration than for the earlier ones. These circumstances suggest that O2 metabolism was a relatively late acquisition and that O2 respiration was made possible by some molecular add-ons to existing metabolic systems.

This contention is supported by family trees of bacteria, which show that O2-users are surrounded by O2-nonusers, as if use of O2 was a later acquisition. Furthermore, O2-releasing photosynthesis used two photosystems, one of which is probably a duplicate of the other, as compared to the single photosystem used by non-O2-releasing photosynthetic bacteria.

This is in agreement with geochemical evidence, which shows that the oxygen content of the Earth's atmosphere rose over time. Starting about 2 billion years ago are the Banded Iron Formations of deposits of Fe2O3, which is insoluble, while FeO, with less oxygen, is. Also, the uranium oxide UO2 is replaced by U3O8.

From chemical-equilibrium considerations, one finds that the Earth's atmosphere would be neutral, consisting mostly of N2 and CO2. Oxygen would be removed by the oxidation of weathering rocks. Thus, around 2 billion years ago, something or other had started producing oxygen, and that was presumably the cyanobacteria.

To sum up, the vestigial feature here is O2-independence by the bulk of the metabolic processes.

References

Archaebacteria, C.R. Woese, Scientific American, 1987(?)

The Phylogeny of Prokaryotes, G.E.Fox et al. (including C.R. Woese), Science, Vol. 209, p. 4455; July 25, 1980

From: Keith Doyle

I know of several individual examples, one of my favorites is the chapter "Nasty Habits" in "The Flight of the Iguana" by David Quammen. He describes the bedbug Xylocaris Maculipennis and how it has adapted a curious way of reproduction, that of homosexual stabbing rape. Apparently some of the various bedbug species make use of a "mating plug" where once a male has mated with a female, the male "seals her shut" preventing other males from mating with her. Some species have adapted around this by stabbing rape, where the male impales the female and bypasses the mating plug. In Xylocaris Maculipennis, this has been taken one step further, where the male will impale and inseminate other males, and the rapist's genes enter the bloodstream to be carried to females by the victim. In this way, the rapist conceives by proxy.

And of course there are other examples, "The Panda's Thumb" by Gould is one of the classics by now, and I expect you'll hear about others.

From: Matthew P. Wiener

Detorted gastropods are another example of brain-dead design. Gastropods are famous for the 180 degree twist they do to their larval bodies, so that their rear ends are sticking out over their heads. So far, this is just weird. What is moronic (were it design) is the fact that some of the gastropods (the detorted ones) then do an untwist, and straighten out their body afterwards.

Note that had Garstang been right about the reason for the twist--it's a survival mechanism for larvae, protecting their heads--then twisting and untwisting makes good design sense. But experiment shows that torsion makes no such difference ... it only makes for good poetry.

From: Paul Keck
Newsgroups: talk.origins
Subject: Re: design in living organisms

I've read that 1 in 3 men will need to have prostate surgery in their lives. Now, everyone look left.. now look right.. One of you will be the lucky man! Can you say endoscopy? How about razor blades?

Chris, you left out the even worse design of having the testes form inside the abdomen, then have to pass through the abdominal wall and down to the scrotum, thereby leaving a weak spot (two, actually) in the wall. This spot, called the inguinal canal, can herniate, allowing the intestines to slop out under the skin. Herniation both screws up the intestine and cuts off/slows the blood flow to the affected testis. Great design.

From: lip@s1.gov (Loren I. Petrich)
Subject: Re: Bad design and vestigial organs

In my article on vestigial features, I had promised to omit the animal kingdom, in the expectation that others would have superabundant animal-kingdom examples. That expectation only partially fulfilled, I will now give some animal-kingdom examples. I hope it is good FAQ material :-)

The wings of flightless birds. For most flightless birds, the wings are non-functional, aside from possible display functions. The only major exceptions are diving birds, like penguins, whose "wings" serve as control surfaces. In some cases, the wings are very small, as for kiwis. The effect is to reduce the number of usable limbs from 4 to 2, which can hardly be called an improvement.

Bird-teeth genes. All the living birds, and all the known Cenozoic fossil birds, are toothless. Most Mesozoic birds and dinosaurs possessed teeth (any toothless Mesozoic birds?). A recent experiment in growing chicken-embryo jaw tissue next to some mouse/rat jaw tissue in a mouse's eye revealed that teeth formed. And the teeth did not look like any rodent teeth, but were peg-shaped with a conical top, just like the fossil bird teeth. The ability to grow teeth was thus preserved for over 65 million years, perhaps as a side effect of certain growth-control genes specifying more essential things.

Extra toes of ungulates. Various hoofed mammals typically have toe bones in addition to those that bear the hooves. This is readily evident on the feet of artiodactyls (cows, deer, pigs, etc.). For equids, two splints are sometimes present alongside the main toe bone. Also, domestic horses are sometimes born with three-toed feet. Relatively recent fossil equids, however, often had three-toed feet, indicating that the one-toed feet of the extant equids is a development of the last couple million years, but that the animals still have the ability to produce three toes per foot.

Solid-color equids having genes for making stripes. The living equids are the domestic horse, its wild progenitors, the donkeys, and the zebras and quaggas. Matings of different breeds of solid-color equids (horses and donkeys) sometimes produce offspring with zebra-like stripes. It is as if the genes for making stripes, which are expressed in zebras, are switched off in the solid-color equids, only to re-emerge in certain circumstances.

Flies growing legs instead of antennae on their heads, and mosquitoes with legs for mouthparts. These "homeotic mutations" suggest that these appendages were originally legs, but that they were specialized to different functions. Removing or disabling genetic instructions which roughly translate into "A limb on this segment is to become an antenna" and "a limb on this segment is to become a mouthpart" leaves the limb following a default instruction that goes something like "a limb on this segment is to become a leg" (it's not even that simple, because insect legs on different segments are often specialized differently). There is another mutation that causes fly larvae to start growing legs on the abdominal segments; this mutation is lethal, but if it was not, then an adult fly would emerge from the pupa with lots of extra legs down its body. The results of these limb-growth-control mutations are consistent with the hypothesis that the original arthropod had essentially identical, unspecialized limbs, which were specialized to different functions, or even suppressed, among its descendants. These limbs would have been specified in cookie-cutter fashion, and the various specializations and suppressions would have resulted from later add-ons to the growth instructions. Interestingly, trilobites and the Burgess Shale arthropods show relatively little evidence of limb specialization/suppression, so the earliest fossils are consistent with the overlaid cookie-cutter hypothesis.

Crab tails. Under their broad, flattened bodies can be found small tails. These are clearly a leftover from when their ancestors had long, thin bodies, as lobsters still do.

Ancestral wing configurations reappearing. Flies sometimes grow a second pair of wings instead of halteres (balancing organs); most other living insects have two pairs of wings. Cockroaches sometimes grow a third pair of wings, like some fossil insects.

Fetal teeth missing from adults. Baleen whale fetuses have teeth and fetal calves have upper front teeth; adult (and probably newborn) baleen whales are toothless (the baleen is not teeth), and cows lack upper front teeth. These teeth never erupt and are resorbed as the fetus grows.

Snakes with vestigial limbs. Boa constrictors have small vestigial hind legs; these may aid in copulating. However, most other species of snakes lack this feature, and seem to do fine without them.

Cetacean hipbones. Some whales have hipbones deep inside their bodies, attached to no limbs. One possible purpose is to serve as an attachment point for muscles that move the penis, however.

Mammal tails, at least in many cases. These are much reduced from the reptilian ancestral form, and when they serve a function, it is usually for whisking away flies (as for horses) or for signaling (consider dogs wagging their tails). New World monkeys, however, use them as an extra limb, and kangaroos have big tails for balancing, so mammal tails sometimes do have important new functions, however. There are some with very tiny tails, like elephants, and some which lack them, such as bears and apes/humans. The ancestral ape was probably capable of brachiating (moving around in trees suspended from tree limbs that one is holding), which gibbons and siamangs still do today. This would have made a tail a nuisance, thus leading to its suppression (the same thing may have happened to the ancestor of the frogs and toads). The disappearance (or only near-disappearance?) of bear tails is less easily explainable, however. But even there, evidence of tails is sometimes present, as in human embryos having tails for awhile. A side effect of a brachiating ancestry may be our ability to point our arms straight upward (in the direction of the head), an ability not as critical for our species as it is for gibbons and siamangs.

Flounder eyes. On sea floors, there live these fish that lie on their sides. They have two eyes -- on one side of their heads. But they start off life with eyes on both sides of their heads, and one eye moves to the other side. Why two eyes instead of one? And why originally on both sides of the head?

Original embryonic eye positions. In human and dog embryos, as in most other vertebrate embryos, the eyes are originally on the sides of the head. However, the eyes move forward as human and dog embryos grow, to make possible binocular vision. One human birth defect is for this process to be incomplete, making the eyes too far apart. Among the vast majority of the animals with backbones, the eyes are at the sides of the head; the main exceptions I know of are the bats, the primates, the carnivores, the owls, and possibly some of the more cerebrally endowed small carnivorous dinosaurs. In their family trees, they are surrounded with eyes-on-the-side animals, suggesting that binocular vision evolved several times.

Giraffe neck lengths. Baby giraffes start out with necks whose relative length is similar to those of other ungulates; it is as they grow that they acquire the relatively long necks that the species is noted for.

Human toes. Our feet have toes, one of which is big and slightly separated from the others. For walking, there is no special need of having a split front end of the foot; it should not be surprising that the toes are small. But they are there, and in most primate species they are much more prominent. In some species at least, the big toe points outward, just like a thumb. Interestingly, in some early hominid species, the toe bones were relatively longer than in our species.

Wisdom teeth. Our jaws are a bit small for these late-erupting teeth; some people have them, while others do not.

Outsized hind legs of some four-legged dinosaurs. Stegosaurus, especially, had hind legs much bigger than its front legs. This is probably a byproduct of being descended from a two-legged ancestor that went back to walking on all fours. Many of the dinosaurs walked on their hind limbs only, with the front limbs remining at various levels of development. In Tyrannosaurus, they are very small, though still there, which has led to the suggestion that they are vestigial. The earliest dinosaurs known, like Herrerasaurus, were like this. Transitional cases? Possibly! Iguanodon or some other such dinosaur apparently walked on two legs when juvenile, and on all fours when adult (and a lot heavier).

[My memory runs out at this point...]

Good sources for some of this material: Charles Darwin's Origin of Species and Stephen Jay Gould's essays, notably Hen's Teeth and Horse's Toes. In addition, studies of embryonic development often reveal an abundance of vestigial features, some examples of which are given here.

On the molecular level again....

An abundance of "pseudogenes" have been discovered, which are not prefaced with a "start" codon, but which have a resemblance to known genes that is too improbable to be coincidence. These are most likely the results of gene duplications and mutations that turned the "start" codon into something else. Thus the DNA-to-RNA transcription system does not "know" that here is a gene to be expressed.

From: huston@access.digex.com (Herb Huston)
Subject: Re: design in living organisms

You can find bad design everywhere in the human body (the wiring of the photoreceptors in the eye and the structure of the knee leap immediately to mind (perched rather precariously for such a supposedly important structure)).

It can hardly be said that the human knee is well designed for kneeling. Prolonged kneeling can lead to an expansion of the bursa in front of the patella, a condition known as housemaid's knee. (Perhaps that's why housemaids are almost extinct.)

Likewise, there's a design flaw in the human elbow. At the knob on the lower end of the humerus the ulnar nerve is exposed just under the skin. A sharp blow by a hard object causes that numbing, painful sensation called "striking the funny bone" (a pun on the name of the bone).

There are some additional design flaws that appear in the manufacturing process of humans: the fetal lanugo, the grasping reflex, the Moro reflex, and the fontanelles. Even the adult human skull is too thin to provide adequate protection to the gigantic brain and the absence of brow ridges leaves the eyes poorly protected.

When can we expect issuance of the recall notice?

From: lip@s1.gov (Loren I. Petrich)
Subject: More vestigial features...

Fused bones. These are bones that start out separate and become knitted together for added strength. Human examples are the skull and the pelvis; birds have several bones in their front limbs (wings) fused.

Bird alula or "bastard wing". A much-reduced digit on the front limb. The two others are retained, though they are fused into one piece.

The Hoatzin chick's claws. The claws on their wing limbs enable them to climb away from potential predators; their presence indicates that all the clawless-winged birds have the potential of growing claws on their wing limbs, which is inherited from their clawed-limbed land ancestors, which were probably small theropod (carnivorous) dinosaurs.

Hollowness of dodo and penguin bones. It is not critical for ground birds to reduce weight with hollow bones of the sort that flying birds have.

Animals which make teeth as fetuses, then resorb them: Baleen whales, anteaters, and some ungulates (cows have upper front teeth which they later resorb).

Gill bars of tetrapod (land-vertebrate and descendant) embryos. The cartilage gill bars appear, only to disappear or be reworked with later growth. Of these animals, only amphibians have gills, and that only in the larval (tadpole) stage. Most adult amphibians and all the rest are air breathers; even the aquatic ones do not grow gills to use underwater.

Aquatic-tetrapod air breathing and land breeding. Largely aquatic animals like sea turtles, Galapagos iguanas, sea snakes, crocodilians, water birds including penguins, phocids (seals, sea lions, and walruses), and cetaceans (dolphins and whales) all have to come up to the surface to breathe; all of them but the sea snakes and the cetaceans lay eggs or give birth on the land. Though the sea snakes and cetaceans are completely aquatic, giving birth in the water, they still have to breathe air, which is a limitation for a completely aquatic animal.

Jaw origins from gill bars. In jawed-vertebrate embryos, the jaws are formed from the gill bars closest to the mouth. In jawless fish (lampreys and hagfish), these gill bars stay gill bars. This circumstance indicates an origin of jaws from gill bars.

The mammalian amniotic sac. This is a vestigial eggshell that surrounds the fetus. Live birth evolved out of retaining an egg inside.

Tadpoles. Immature frogs go through this phase, in which they look and act much like fish.

The aquatic embryos of land salamanders, which live on the land from hatching.

Tails of human embryos. Though tails are a nearly universal vertebrate feature, and are present in all the embryos, they are lost in later growth in our species and the most closely related ones (the apes), leaving only a tiny bone on the pelvis, the coccyx.

Rudimentary legs of some snakes (boas, etc.). Other species of snakes seem to do fine without them.

The small lung of snakes with only one lung significantly large. It is an inheritance from two-lunged ancestors.

Small wings of flightless female moths in certain species. In most other species, as with winged insects in general, both sexes, and not only the male, have functional wings.

Stumpy tails and other such features of some domestic animals bred to have none.

Nonfunctional pistils in male flowers. Since the predominant configuration of flowers is to have both sexes of reproductive organs (stamens and pistils), the pistil of a flower with only stamens functional is vestigial.

Certain plants [Serophulariaceae (Darwin's Origin of Species)] have reduced stamens.