http://www.talkorigins.org/faqs/jury-rigged.html
This is strong evidence against biblical creationism. It isn't as strong an evidence against intelligent design however, because even ID advocates such as Michael Behe and William Dembski claim that design doesn't imply perfection. So this is more a punch against biblical creationism. It's still strong evidence for evolution. Any rebuttals?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.
