It's just that the paper seems to be setting up and saying, "this is what we need to figure out, here are some first steps". And this is pretty typical within the scientific literature.
a couple of things about smiths paper.
first complexity.
smith uses the word then mentions transitions., then lists those transitions.
one of those is the acquisition of language.
i wouldn't necessarily call this an increase of complexity, but smith does.
anyway, smith is right in stating complexity is very hard to define.
second is the date, this stuff was still being passed around as late as 1995.
in other words "these are the problems, and this is what needs to be done" was current as of then.
at the very same time we had people running around saying evolution is a fact, we have it solved, and other etched in stone types of things.
To quote PZ Myers:
It’s a superficial ploy creationists play. They don’t have any scientific literature of their own, so they go rummaging about in the genuine scientific literature and start pulling out fragments that show disagreement and questions in the evolutionary community. And that is so trivial to do, because they don’t grasp something obvious and fundamental: every science paper has as its throbbing heart a question and an argument. Seriously. Every single paper on evolution is arguing with evolution, probing and pushing and testing. I am not at all impressed when some clueless dingbat pulls up Alberch’s paper titled “Problems with the interpretation of developmental sequences” and crows about finding a paper that talks about “problems”. Problems are what we’re interested in.
not everyone that questions current thinking on this subject is a creationist.
eldredge, gould, ayala, koonin, noble, none of these people are creationist, but they had serious questions about what was then known about current theory.
koonin has the hardest job, because he wants to integrate ALL of life into the theory, not just plants and animals.
this is why he says darwinism belongs in a museum, because it only dealt with certain types of life, not all of it.
genomic research, molecular biology, and statistical physics is going to allow this to happen
Let it be known that my opinion towards you is considerably less hostile (and justifiably so) than PZ's opinion towards the person he was referring to, and I have nothing to say about your motives.
like i said before, many, many, times, i'm not arguing for a god, but i do have an open mind.
Well great. Then do you accept that Koonin accepts common ancestry, descent with modification, and natural selection? And do you accept those things?
yes, i believe koonin publicly endorses evolution.
Yes, I did. It was dealing with a specific issue in a specific branch of Drosophilia. We can expect this kind of thing to pop up every once in a while, mainly because taxonomy is not as precise as genetics is when it comes to phylogeny.
the part i posted was in direct reference to the TOL and made no mention of drosophilia.
let's see, ah:
At least three processes complicate such a view of a tree of life, horizontal transfer, symbiogenesis, and differential lineage sorting of genes. Each of these processes are at odds with fundamental assumptions of the Modern Synthesis.
...
Nevertheless, molecular characterization of transposable elements in the late 1970s finally undermined the view of the genome as a static, well-organized library of genetic information
...
Similarly, modernist preconceptions led some to discount the importance of endosymbioses in the origins of new life forms, like eukaryotes. Broad theories of endosymbiotic origins for species had been suggested in the late 19th and early 20th Centuries [7], but were ignored save for a few well-established cases like lichens. By the 1980s, the evidence for symbiogenesis in major cell biological events was voluminous
...
These phenomena complicate the tree of life. Rather than a graph connecting species, the tree of life itself is hierarchical: A universal tree of species is largely a human-imposed ideal because the components of any particular species have evolutionary histories that are not congruent with each other.
-The new biology beyond the Modern Synthesis.htm
as you can see, there is no mention of drosophilia
and?
any comment on why there was a linearly decline in fitness, not in 5 or 6, or most, but in ALL lines tested?