From: ingles@engin.umich.edu (Ray Ingles)
Subject: Bad design and vestigial organs
Date: Tue, 17 Nov 92 00:15:02 EST
Organization: University of Michigan Engineering, Ann Arbor

In article <MMF=kw-@engin.umich.edu> ingles@engin.umich.edu (me) writes,
concerning old posts about brain-dead design:
>
> I saved a few. I tacked on these last couple posts, too. I'll post them
>after this article; I do;t have time to keep a FAQ, but maybe someone will
>be moved to store these for posterity....
>
> Ray Ingles
> ingles@engin.umich.edu
> 
> "Um, you mean I shouldn't have folded the disk in half before I put it in
>the drive?" - actual user quote

Article: 27932 of talk.origins
From: lip@s1.gov (Loren I. Petrich)
Newsgroups: talk.origins
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)




Article: 32071 of talk.origins
From: colby@bu-bio.bu.edu (Chris Colby)
Newsgroups: talk.origins


	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's book "The
Panda's Thumb" for an engaging discussion of this case). Again,
this is not good design.

In gastropods (ex. snails) there is an embryological process called
torsion. During torsion, the anus of the animal is flipped to
the right and up and flopped down on top of the head. This is so both
"ends" of the organisms point out of the shell. A side effect of 
torsion is reduction of organs on the right hand side of the body
(the side that is interior to the bend). Now, some gastropods
(slugs) have abandoned their shelled existence (due to the evolution
of toxicity as protection) and yet they undergo torsion and then
de-tort in their ontogeny. In some cases the right hand side 
remains "withered". Going through a process of development to
enable an organism to live in a shell it doesn't't have, then 
"correcting" this "mistake" is not good design.

Chris Colby
email: colby@bu-bio.bu.edu 



Article: 32075 of talk.origins
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.

 [Sorry 'bout the duplication of the gastropod torsion thing. I figured
Matthew should get some credit. Chalk it up to a vetigial trait...:-> ]

 Ray Ingles
 ingles@engin.umich.edu