Here I go into great detail describing why UCD does not predict any alleged nested hierarchy. Namely, if you look at humans within its own specie we see violations all over the place. It’s possible for someone to have a trait (or genetic sequence / gene), have a brother that doesn’t have this trait, yet have a cousin that has this exact same trait (or genetic sequence). This produces a violation. It’s possible for someone with a much more distant relationship to also have this trait that the two brothers don’t share. Within a specie we see violations all over the place, nowhere do we see any such nested hierarchy. Evolution does not produce any such nested hierarchy within the human specie, likewise it would not produce any such hierarchy when they speciate. We see violations all over the place within a specie and those violations won’t just disappear when the specie speciates. Despite the fact that UCD does not predict this alleged nested hierarchy, this alleged nested hierarchy resists horizontal gene transfer as being a significant factor in producing and spreading genetic variation (ie: new traits). It makes it much more difficult for evolutionists to explain away genetic diversity through horizontal gene transfer, which they would do if the data allowed it. The evidence was designed to resist naturalistic explanation. For more details, see the above link and read my posts (for this post is just very very general, I go into far more details within that link). Also note, much of this reasoning has been inspired by the book, “The Biotic Message” by Walter James ReMine, who, like I, believes the evidence was designed to resist naturalistic explanation.

http://telicthoughts.com/?cat=12

http://www.overwhelmingevidenc.....omment-193

http://www.overwhelmingevidenc.....omment-428

Oh, and personally I’d interpret that “Bushes in the Tree of Life” referenced in comment #3 by Jehu as possibly supporting multiple LUCAs.

The botom-line is Common Descent can live with it or without it. Darwin was well aware of that.

Extinction, as we have seen in the fourth chapter, has played an important part in defining and widening the intervals between the several groups in each class. We may thus account for the distinctness of whole classes from each other- for instance, of birds from all other vertebrate classes from each other- by the belief that many ancient forms of life have been utterly lost, through which the early progenitors of birds were formerly connected with the early progenitors of the other and at that time less differentiated vertebrate classes.

IOW if all the alleged transitionals were still alive such distinct categories would not exist.

What nested hierarchy does demonstrate is that the same evidence can be used for two opposite PoVs- both Mayr and Simpson recognozed that:

One would expect a priori that such a complete change of the philosophical bias of classification would result in a radical change of classification, but this was by no means the case. There was hardly and change in method before and after Darwin, except that “archetype” was replaced by the common ancestor.– Ernst Mayr

(“the hierarchy looked the same as before even if it meant something totally different.” – Simpson)

Well sir, an omnipotent creator could theoretically be creating a brand new universe, in place, with modifications, once every nanosecond or even more often. But if he is he’s sure doing a good job in making it look like it’s been here a long time and evolves according to a self-consistent set of natural laws – one of those laws being the law of biogenesis. How do you rationally determine when and how many special acts of creation there were? Occam’s Razor would have us make those acts of special creation as few as possible. I count only one that was strictly required – the universe itself but I think life was created once too for a grand total of two separate acts of special creation.

“He asserted that there is realm of Forms or Ideas, which exist independently of anyone who may have thought of these ideas. Material things are then imperfect and transient reflections or instantiations of the perfect and unchanging ideas.” (source: wikipedia)

Every living thing thus far examined uses virtually the same genetic code. Couple this with the law of biogenesis and you have an exceedingly strong case for common descent IMO.

If gradualism were indeed true in all cases a nice, neat phylogenetic tree with no ambiguity should be easy to construct today with molecular homology serving as a twin nested hierarchy confirming phenotype homology. In point of fact it isn’t easy and ambiguities are common. Convergent evolution, horizontal gene flow, epigenetic factors, and very limited understanding of what all contributes to phenotype expression at the molecular level mucks it up. Furthermore, the fossil record is not a record of gradulism, it’s a record of saltation.

This raises the question of how saltation can occur. I suspect the answer to that lies in a nested hierarchy of phenotype control mechanisms. Regulatory regions in individual genes are the lowest level. These are capable of fine tuning of a species but not saltation. A higher level of control would be genes that regulate the expression of groups of genes but I don’t believe those are capable of saltation in a general case as it doesn’t provide a mechanism for reproductive isolation. Gould recognized these problems and came up with a spatial theory of reproductive isolation – small populations get cut off by physical boundaries, genetic drift takes over, and you can get a new species in geologically short amount of time with little evidence of it in the fossil record because the population was so small. I find that rather contrived to preserve a dogmatic belief in gradualism.

More likely, IMO, is the existence of an even higher level control mechanism. Consider coding genes as components in a Lego set. You can build all kinds of different structures by changing their relative number and arrangement. While it’s true you can gradually remove and add components to change a bridge into an igloo it’s a lot easier if there’s a master plan for an igloo, a master plan for a bridge, and you set out to build one instead of the other from the ground up.

I suspect the master plan, the highest level in the control heirarchy, lies in the structure of chromosomes. Chromosomal rearrangements typically cause reproductive isolation in one fell swoop through reduced or zero hybrid fertility. Large chunks of genetic material can be rearranged instantly without change in lower level hierarchies through chromosome reorganization. Position effect is well enough established. Moving a gene from one spot to another on a chromosome causing phenotype change has been amply demonstrated. Chromosome organization varies widely among different species while the basic building blocks remain more or less a constant set. Is that wide variance in chromosome organization a meaningless thing brought about by random events? A higher level hierarchy of junk DNA? I dont’ think so.

So in the case of the platypus, if all or most of the basic building blocks are shared between mammals and birds, and all the building blocks were present in their common ancestor, then each is distinguished by a master plan describing how to arrange the blocks. Thus mixing and matching large phenotype characteristics is possible in saltational events. For instance you could mix things up to get an egg bearing animal that produces milk, has webbed feet like a duck, has limbs positioned at the sides like a lizard, has leg spurs like a rooster tipped with snake-like venom, has electroreception in its snout like a shark, thermoregulates body temperature much lower than birds or mammals, has a cloaca like a reptile, and (drum roll please) has sex determination chromosomes part bird and part mammal.