Squeers,
I think you confuse two things, probably because I myself did not make that distinction clear enough:

(1) the “objective truth” about reality investigated by science, i.e. about physical reality independent of the subjective (social etc) context;
(2) the “objective truth” about the structure of all Reality, i.e. whether or not it is reducible to physical reality.

In both cases “objective truth” coexists with “subjective - or observer dependent - truth”, although in (2) the subjective side is more pronounced than in (1): As I said elsewhere, “God created man” and “man created God” are two sides of the same coin. In case (1) I do not think observer-dependent and independent “truths” play such symmetric roles, the Copenhagen school notwithstanding.

The dispute in (1) is between scientists and “social constructivists of science” (related to the two C.P. Snow cultures?), the dispute in (2) between theists and atheists. Although elsewhere I made it clear where I stood in (2), my concern in the last two posts was along the lines of (1), in defense of the objective character of truth pursued by scientists.

Defence of the objective character of “scientific truths” was behind Sokal‘s “hoax” article, and triggered the “science wars”. This had nothing to do with the disputes sub (2): most of the “science wars warriors” from both sides were atheists (agnostics) and politically leftist.

“(T)he laws of physics are real … in pretty much the same sense (whatever that is) as the rocks in the fields, and not in the same sense … as the rules of baseball. … The objective nature of scientific knowledge has been denied … by Bruno Latour and (as I understand them) by influential philosophers Richard Rorty and Thomas Kuhn, but it is taken for granted by most natural scientists (the atheist physicist Steven Weinberg in “The Sokal Hoax”, U. of Nebraska 2000, p. 155).

Apparently our sympathies are for the opposite sides both sub (2) and sub (1). Did I understand you properly?

George,
This debate has been going on since the Greeks, through Kant to the pomos. Derrida also debated Searle on the subject and for my money won on points. I don't have a decisive stand on reality. I've said above that I'm interested in materialism, which implies absolute subscription to objective reality, though my materialism is highly qualified. In the end we can't know if objective reality is "true"; what does that mean anyway? Truth is a human construct. I believe in our reality to the extent that it is probably the only reality we will, as humans, ever know, notwithstanding that it is finite and ergo that there are limits to its "reality". Reality is "objective" to the extent that it objectifies the human condition, how can we know if we objectify it? Science cannot pretend to transcend that horizon, though it elides it experimentally--often irresponsibly--the method proving productive of technologies that far outstrip our ability to assimilate. Embracing these technologies, we are that much more remote from the "real" conditions of physical life, which are ever more degraded. Conversely, religion seduces us with the prospect of "real" ethereal realms, beyond this veil of tears, also concomitantly denigrating physical reality.
I have no idea of the validity of "reality investigated by science", but even if reality is objectively perceived, I doubt scientists' ability to understand it objectively, outside human constructs. Moreover I'm critical of science's blind questing, often both remote from human cares and exacerbating of them.
I do not camp with the constructivists, however; I like to think that it is possible to see through ideology, or at least to perceive ideology as the opacity that prevents us from appreciating the world as it is, beneath cultural rationalising.
So I don't take a definitive stand on truth or reality. I simply don't know and don't believe in belief. The fact that I comply with the constraints of reality doesn't mean I "believe" in it, just that I'm obliged to observe those limitations. Cultural reality is definitely mutable, and we should be bringing it down to Earth.

Philo,

You asked about new genes, I told you.

If you look up horizontal gene transfer you will see how new metabolic capacities can be transferred between species having been rough-hewn in the bacterial cauldron. Viruses are a major vector and arguably the principal "cauldron" in which new highly active promoter sequences are generated.

The "source" of new genes is mutation and selection, and the starting point for this in existing biology is *any* unused but transcribable sequence.

Now, one new gene does not make a new species (except in special cases), nor does altering the expression in a recipient.

Given that more and more can and do accumulate, along with viral sequences including active promoters, do you propose that a lineage *cannot* accumulate enough to enable a basis for selection or even for eventual divergence into a new species?

Very few coding genes differ (and often barely so) between (say) chimps and humans. The likely source of our genuine developmental divergence from chimps lies in the switching and regulation of coding genes.

This is achieved through such means as cis and trans-activating factors binding directly to DNA to either enhance or inhibit transcription. Short pieces of RNA binding to the transcript achieve similar roles. These sequences are more variable within species than coding regions and given this placticity, more able to be altered by viral inserts, run-of-the-mill mutation events and recombination in every generation. All activating/inhibiting and transcription factors bind to *all* DNA at low levels. If the transcription product is in any way beneficial, it is likely to be passed on, if merely neutral, it is still likey to pass on for many generations. In either case mutations will occur and more/less/more specificity can be selected in the ordinary way.

It is hardly a mystery where new genes come from.

As for all those intermediate organisms, why should they coexist but briefly? In the period that they overlap, they are not as innovative in their capacities as their divergent subgroup, nor as optimised for old conditions as their ancestors. Look up punctuated equilibrium.

Rusty

Philo,

In continuation, and sorry about the hiatus:

Some speciation events are driven by errors in existing genetic material. Horses and donkeys have sufficiently similar genomes that they can produce a (nominally) sterile hybrid. The difference is a recombination error resulting in the fusion (fission?) of two chromosomes.

Simply by having a mismatch in chromosomes number from each parent, with all obviously critical genes otherwise present, makes interbreeding between the divergent group and the parent population virtually impossible. hence speciation with hardly any change in the number of genes, possibly even a small reduction.

A feature corresponding to what *we* might regard as a genetic disease separates these species. Both with us to this day.

Hope this helps.

Rusty,
- "Horses and donkeys have sufficiently similar genomes that they can produce a (nominally) sterile hybrid. The difference is a recombination error resulting in the fusion (fission?) of two chromosomes."

I do not believe horses and donkeys mate in the wild envoronment to produce mules; that is the reason donkeys are identifiable and horses are identifiable. However the chromosomes in a mule are not new (original) material just the combination of the parent are not compatable to establish a new species

Rusty,

The source of new information is published, however, requires some knowledge of genetics to fully comprehend.

Philo probably will try using the same tired old tactic of debating the issue of evolution on some obscure detail where most lay people have limited knowledge, and thus sound authorative.

He tries to sound unbiased by "I believe evolution is probably the most likley process of life" as if it was one of many of which scientific opinion was still out, but completely fails to give any other process with any probability.