In the beginning God created.... Genesis 1:1
In the article below, from a secular site, one can see that TE's are proof of DESIGN for functionability...and the ability to produce different shapes, sizes and colors. The reason it is a problem for evolution is because it undermines random glitches/changes which undermine the core of neo-darwinism and Richard Dawkins....All this change is DIRECTED, for different shapes, sizes and colors for the blooming rose of creation WITHIN each kind....which stays it's kind.
"During the past century, discoveries that have challenged the gradualist
view of evolution have been sidelined, forgotten, and derided.
This
includes the work of 20th-century geneticists such as Hugo de Vries, one
of the rediscoverers of Mendelian genetics and the man who gave us the
term ‘mutation’, or Richard Goldschmidt, who distinguished between
microevolution (change within a species) and macroevolution (changes
leading to new species).
Barbara McClintock, one of the giants of 20th-century genetics, has 
not
been accepted as posing a viable alternative to dominant theories of
evolution. McClintock won the Nobel Prize in 1983 for her discovery during the 1940s of rapid genetic changes in maize plants that were definitely not random.
In 1944, McClintock began mating maize plants with genomes configured so
that both parental pollen and ovule cells contained broken chromosomes.
The result of these experiments created what has been described
as ‘a genetic earthquake’ in the fertilized embryos. Many could not
produce viable maize plants, and those that could grow to maturity often
exhibited variegated patterns of coloration in the stalks, leaves and
kernels.
material that were unlike any previously discovered. She demonstrated that these ‘controlling elements’, as she came to call them, had previously been dormant in the maize genome and were activated in response to ‘genome shock’ from ongoing cycles of chromosome breakage and repair.
This discovery revealed an entirely new mechanism of genetic 
regulation
and variability: maize plants were rapidly changing their own genomes
through transposable controlling elements (TEs). And moreover, TE
changes were nonrandom in two ways.
Firstly, the same DNA
element could insert repeatedly at new target sites; and,
secondly, TE
mobility and mutagenic activity was activated by specific organismal
stress conditions.
There are multiple types
of TEs, including purely DNA-based ‘transposons’ as well as two
different types of ‘retrotransposons’, which use RNA intermediates to
move to new locations in the genome.We might expect that McClintock’s discovery of TEs and their rediscovery
across all forms of life would have unleashed 
serious questions for
established views of evolutionary change.
Instead, her findings were
ignored. My own belief
is that the reason for this wilful neglect lies in the basic
philosophical foundations of mainstream thinking about evolution, which
requires a purely physical explanation for all evolutionary processes.
The fact that TEs respond to stress indicates that they are regulated
biological entities that play a sensory-guided role in survival and
reproduction. The notion of controlled biological processes at the core
of organic evolution is plainly incompatible with a purely physicalist
explanation, such as random mutations plus natural selection."
aeon/J.A.Shapiro
