From: colby@bu-bio.bu.edu (Chris Colby)
Newsgroups: talk.origins
Subject: evidence for jury rigged design
Date: 28 Jan 93 22:55:22 GMT
Organization: animal -- coelomate -- deuterostome

This 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 and Keith (?) -- if you wrote this, write
me so I can credit you with your example)

___________________________________________________________
	Many organisms show features of appallingly
bad design. This is because evolution via natural selection
cannot construct traits from scratch; new traits must be mod-
ifications 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 _Cnenidophorus_,
only females exist. Fertility in these lizards is increased when
another lizard engages in pseudomale behaviour and attempts to
copulate with the first lizard. These lizards evolved from a sex-
ual 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 partheno-
genetic 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 med-
ical 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 vertabrates) fingers are made of. The thumb is con-
structed 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.


	Refs:

	_Bacterial Evolution_, C.R. Woese, Microbiological Reviews,
Vol. 51, No. 2, p. 221; June 1987

	_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


/Loren

----------------------------------------------------------------------
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 concieves 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.

Keith

---------------------------------------------------------------------
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.
-- 
-Matthew P Wiener (weemba@sagi.wistar.upenn.edu)

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.

Paul Keck.  I'm not a strangulated hernia, but I play one on TV.


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 abundace 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.

/Loren


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

In article <102252@bu.edu> colby@bu-bio.bu.edu (Chris Colby) writes:
>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 house-
maids 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?

-- Herb Huston
-- huston@access.digex.com


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

/Loren Petrich, the Master Blaster
/lip@s1.gov

Chris Colby 	---	 email: colby@bu-bio.bu.edu	---
"'My boy,' he said, 'you are descended from a long line of determined,
resourceful, microscopic tadpoles--champions every one.'"
 	--Kurt Vonnegut from "Galapagos"