"Conversely, no reliable observation has ever been found to
contradict the general notion of common descent."
Ryan seems to be ignorant of some of the facts:
"Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life's history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted. Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences. Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identification of new molecular characters will be crucial to future progress."http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1637082
While they are promising to resolve the contradictions of the genome evidence. It is never the less a reliable observation that contradicts a single TOL.

“A prime example is provided by
the chronically misunderstood Second Law of Thermodynamics,”
Ryan shows his own misunderstanding of this Law.

"if there is no
external source of energy" (“a closed system”),
The definition of a, ("closed system") is not "having no external source of energy" as he suggests. A closed system is a, "mechanism (system), that doesn't have any source of energy. I point this out,
because he isn't always clear that a system (mechanism) is necessary to complete the needs to
overcoming entropy. Energy alone increases entropy.

"Local increases in order are not precluded
(ornate snowflakes still form from water vapor),"
This is another misunderstanding by Ryan.
Water vapor freezing into snowflakes is NOT an increase in order.
The order is already present in the physical order of water molecules and the physics surrounding freezing. . The freezing process just (reveals) that already established order! That is why it is predictable and consistent.

"If the Second Law of
Thermodynamics implied that all natural increases in order
were impossible, then it would be incorrect. It does not and
(so far as we know) is not. The broader point is that
invoking the Second Law of Thermodynamics as an
argument against evolution reveals a misunderstanding of
both the scope of this particular law and of the meaning of
“law” in science generally."
Ryan misunderstands how this law is applied in an argument
against evolution.
Mechanisms (systems), fueled by energy. can over come entropy.
However In biological Evolution, without a complex mechanism, which turns energy into
useful work , work that makes self regeneration and more complex designs possible. Designs hat functions better in changing environments.
Therefore Biological Evolution needs established (mechanisms or systems)
before it can work it's magic. This (SLofT) also precludes (random mutation) from
being the source of ( complex specific, design and order). Which then precludes a Universal Common ancestor. Howie Motz