Intelligent Design Theory: Science or Religion?

Since acorn worms and the human lineage diverged 570 million years ago, pharyngeal slits for filtering food evolved into gills for extracting oxygen, and later into today's human upper and lower jaw and pharynx, which encompasses the thyroid gland, tongue, larynx (voice box) and various glands and muscles between the mouth and the throat. Humans and other terrestrial vertebrates actually initiate vestigial gills while embryos, though they disappear quickly and rarely persist in infants.
"The presence of these slits in acorn worms and vertebrates tells us that our last common ancestor also had them, and was likely a filter feeder like acorn worms today," said Daniel Rokhsar, one of the leaders of the sequencing effort and a UC Berkeley professor of molecular and cell biology and of physics. "Acorn worms are marine invertebrates that, despite their decidedly non-vertebrate form, are nevertheless among our closest invertebrate relatives."

Read more at: http://phys.org/news/2015-11-sequencing-genomes-closest-wormy-cousins.html#jCp

In 2007, Columbia University philosopher of science Philip Kitcher published his Oxford University Press book Living with Darwin. Citing the mass of "genomic junk" that "litters the genome," Kitcher announced, "The most striking feature of the genomic analyses we now have is how much apparently nonfunctional DNA there is."4 In his view, "From the Darwinian perspective all this is explicable," but "if you were designing the genomes of organisms, you would certainly not fill them up with junk."5
Just Kidding -- We Anticipated Function!

When ENCODE's findings were published, many evolutionists reacted harshly to the conclusion that virtually our entire genome is functional. Others, however, realized that it would be sage advice to switch their bets, or simply place new ones alongside the old.

For example, a 2014 paper in Biology & Philosophy initially claimed that "junk DNA seems at odds with the view that the genome is ... the work of an intelligent force or designer," but then argued that a junk-free genome "is compatible with evolution by natural selection," because "we could expect natural selection to evolve lean genomes."6 According to this posturing, whether our genome is full of junk or devoid of it, evolution wins.

But first prize for betting on both horses goes to Richard Dawkins. In his 1976 book The Selfish Gene, Dawkins famously argued that "a large fraction"7 of our genomes is useless parasitic DNA, and that Darwinian evolution explains why:

The true "purpose" of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.8
Again in 2004 he railed against "creationists" on the basis of our junk-laden genomes:
[C]reationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.9
As recently as 2009, Dawkins adopted the incredible position that "the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes."10
In September 2012, however, Dawkins changed his tune dramatically. Just one week after ENCODE's results were published, in a debate against Britain's chief rabbi, Dawkins declared that ENCODE's results are precisely what "Darwinism" (in Dawkins's own words) predicts:

There are some creationists who are jumping on [ENCODE] because they think it's awkward for Darwinism. Quite the contrary, of course, it is exactly what a Darwinist would hope for -- to find usefulness in the living world.11
He went on to say, "[W]e thought that only a minority of the genome was doing something, namely that minority which actually codes for protein. And now we find that actually the majority of it is doing something." Under Dawkins's newly reformed view, "the rest [of the genome] which had previously been written off as junk" is now understood as "the program" that's "calling into action the protein coding genes."12
It's as if Dawkins's decades of arguing that our genome is full of junk never happened.

So I have no idea how to sum this up, except to say if you still think antibiotic resistance follows a creationist ‘model’, then you’re an idiot.

So I have no idea how to sum this up, except to say if you still think antibiotic resistance follows a creationist ‘model’, then you’re an idiot.

Although the consortium claims they are far from finished with the ENCODE project, many reactions to the published papers and the news coverage that accompanied the release were favorable. The Nature editors and ENCODE authors "... collaborated over many months to make the biggest splash possible and capture the attention of not only the research community but also of the public at large". The ENCODE project's claim that 80% of the human genome has biochemical function was rapidly picked up by the popular press who described the results of the project as leading to the death of junk DNA
However the conclusion that most of the genome is "functional" has been criticized on the grounds that ENCODE project used a liberal definition of "functional", namely anything that is transcribed must be functional. This conclusion was arrived at despite the widely accepted view, based on genomic conservation estimates from comparative genomics, that many DNA elements such as pseudogenes that are transcribed are nevertheless non-functional . Furthermore the ENCODE project has emphasized sensitivity over specificity leading possibly to the detection of many false positives.Somewhat arbitrary choice of cell lines and transcription factors as well as lack of appropriate control experiments were additional major criticisms of ENCODE as random DNA mimics ENCODE-like 'functional' behavior.
In response to some of the criticisms, other scientists argued that the wide spread transcription and splicing that is observed in the human genome directly by biochemcial testing is a more accurate indicator of genetic function than genomic conservation estimates because conservation estimates are all relative and difficult to align due to incredible variations in genome sizes of even closely related species, it is partially tautological, and these estimates are not based on direct testing for functionality on the genome.
Conservation estimates may be used to provide clues to identify possible functional elements in the genome, but it does not limit or cap the total amount of functional elements that could possibly exist in the genome. Furthermore, much of the genome that is being disputed by critics seems to be involved in epigenetic regulation such as gene expression and appears to be necessary for the development of complex organisms. The ENCODE results were not necessarily unexpected since increases in attributions of functionality were foreshadowed by previous decades of research.
Additionally, others have noted that the ENCODE project from the very beginning had a scope that was based on seeking biomedically relevant functional elements in the genome not evolutionary functional elements, which are not necessarily the same thing since evolutionary selection is neither sufficient nor necessary to establish a function. It is a very useful proxy to relevant functions, but an imperfect one and not the only one.

Then this creator has taken a qilly nilly approach in the development of lif on earth but has engineered "In" certain expressions that result in resistance (while at the same time the organism can often develop a semi lethal physical condition)

The fossil record is full of "throwaways " of organisms.
We use these as "tools"for exploration .

And many 'fully lethal' ones

We are all throwaway organisms. Why is death pre-programmed?
Maybe as a tool for exploration.

just as you have now (I think) argued from both sides

The decrease of size of the mandible isn't necessarily evolutionary. A hard diet increases the growth of the mandible.

the human diet has gone softer during its history.

This isn't necessarily an example of selection.

Dont confuse my disrespect for what someone like Dawkins uses in his ad-hominems as agreement with your pov.

Leadfoot Quote:
"We are all throwaway organisms. Why is death pre-programmed?
Maybe as a tool for exploration."

.Once again, please explain where youre going here with this?

There is always an alternative explaination.

Quote:

The decrease of size of the mandible isn't necessarily evolutionary. A hard diet increases the growth of the mandible.

the human diet has gone softer during its history.

This isn't necessarily an example of selection.