Thinking about the subject, I thought of another problem with ID’s analogies and their comparisons with things that are known to be intelligently designed.
One of the things that ID proponents sometimes predict is “junk DNA”. Even after asking for several years I can’t figure out why ID predicts this. In Edge of Evolution, Michael Behe says this,
But in fact, DNA isn’t exactly like a blueprint. Only a fraction of its sections are directly involved in creating proteins and building life. Most of it seems to be excess DNA, where mutations can occur harmlessly. Edge of Evolution, p. 66
Indeed, various studies have proposed differing levels of so-called “junk DNA”. Yes Virginia, there is junk DNA. Even the ENCODE project which uses a definition of functional so lose as to be almost meaningless has only about 80% of human DNA as “functional”.
A more recent study (here) says that less than 10% of the human genome is functional.
A little over 1% of human DNA accounts for the proteins that carry out almost all of the critical biological processes in the body.
The other 7% is thought to be involved in the switching on and off of genes that encode proteins — at different times, in response to various factors, and in different parts of the body. from ScienceDaily
That’s a huge problem for Intelligent Design advocates.
They often compare living systems to human designed systems. The logic is that human designed systems are complex. DNA is complex, therefore it must have been designed by something intelligent.
The problem is that for the things humans design, we are WAY better designers. Imagine if your brand new 2 Terabyte hard-drive barely had 20 gigabytes of free space, because the rest of the space was take up with unremovable junk. You’d need a multi-terabyte HDD just to install Windows and you can forget about it running quickly.
What if your car had to lug around an extra 20% more mass? Mass that didn’t do anything, it was just there. Ruining your gas mileage.
What if you had to by twice as much food because half the food was just junk?
Human designers are pretty smart. Many of the things we use frequently have been optimized for decades. Cars today get twice the gas mileage with twice the engine power than cars even 30 years ago. Computers today are hundreds of times faster, while using a tenth of the power of computers from even 15 years ago. I remember in 1989 or so, I bought a 20 megabyte HDD for about $400. Now, I can buy a drive with 10,000 times the storage space for less than $75.
One would think that an intelligent designer of organisms would strip the system down to a bare minimum. That would reduce energy cost overhead. It would be simpler. It wouldn’t have the chances for all those annoying atavisms like humans with a tail and whales with back legs. It would be clean, efficient, and functional.
Oh wait, humans have designed a living cell. 
We report the design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.
And there’s some other instances of humans putting custom DNA into organisms as well. This may be a new industry, one of the authors of that last paper thinks so, since he started an entire company devoted to the process.
Anyway, this is really a huge problem for ID. If they want to use analogies or comparisons to human designed systems, then they need to explain why their super-intelligent designer (who can design and construct a universe and everything in it) doesn’t optimize. Sure, they can explain it away, but they need to so in a robust fashion rather than “Who can know the mind of
god… excuse me.. the designer.
(2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLoS Genet 10(7): e1004525. doi: 10.1371/journal.pgen.1004525
 D. Gibson et al., Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome, Science 329, 52–56 (2010).