This is my final posting debunking professional climate denier Joanne Nova’s “The Skeptics Handbook.” 
Nova's final pseudo-scientific arguments is greenhouse signature.
The greenhouse signature argument boils down to the following:
Because weather balloons haven’t yet been able to locate the “hot spot” – a patch of air above the tropics that should show signs of greenhouse gas-induced warming (hence, the greenhouse “signature”) – there must be something else causing the warming. This was somehow also proof that the models had it all wrong – since they had predicted that, in the tropics, the warming of the troposphere should have been larger than that of the surface.
For a relatively straightforward explanation of why this view is flawed, check out this helpful fact sheet  written by several Real Climate bloggers and their colleagues (also, read this post ). In addition to debunking many of Nova’s arguments about the supposed fallibilities of climate models, it also shows that there is “no fundamental discrepancy between modeled and observed tropical temperature trends when one account for: 1) the (currently large uncertainties in observations; 2) the statistical uncertainties in estimating trends from observations.”
Let's say you don't buy the climate model explanation; there is still another, arguably better, way of measuring tropospheric temperature changes in the tropics: using thermal winds (which, not surprisingly, Nova dismisses as simply using “windgauges to measure the temperature”). Here are some of the advantages of using this approach, as laid out by P.W. Thorne in a recent article in the journal Nature Geoscience  (sub. required):
"In order to gauge upper air temperature change in the tropics in a fundamentally different way, Allen and Sherwood exploit the thermal wind relationship, in which vertical gradients in wind are linked to horizontal gradients in temperature. At first glance this seems a rather convoluted way of measuring temperature change, but on closer inspection this methodology may have some compelling advantages. In particular, whereas temperature measurements have relied on an ever-evolving technology, wind measurements are supported by ground-tracking and, more recently, global positioning satellites. The up shot? There are approximately ten times fewer discontinuities in the wind records than the temperature records, making wind measurements a potentially more reliable indicator of long-term trends than temperature measurements."
While there are also some clear disadvantages – the wind-temperature relation tends to break down near the equator and winds don’t tell us anything about absolute temperature trends, for example – thermal wind measurements are a good bet for multi-decadal climate timescales. And, indeed, they have already helped explain the supposed greenhouse “signature” conundrum:
"So are we any closer to resolving the riddle of tropospheric temperature change? It seems we're getting there. Allen and Sherwood give evidence for a strong warming in the tropical upper troposphere, providing long-awaited experimental verification of model predictions. Furthermore, the warming they observe reaches its maximum just below the tropical tropopause. Such amplification of surface warming is expected on theoretical grounds, and is indeed found on monthly to inter-annual timescales by both models and observational estimates. However, it has been absent in almost all observational estimates on decadal timescales — upon which non-climatic artefacts project most strongly. The new analysis adds to the growing body of evidence suggesting that these discrepancies are most likely the result of inaccuracies in the observed temperature record rather than fundamental model errors.”
That should about do it for Nova’s four supposedly unassailable points – the “only 4 points that matter,” as she puts it. In most cases, I’ve only touched on the surface of the science; for more, you should head over to Grist, Real Climate, NASA’s Goddard Institute for Space Studies (GISS) website and (the many) others who are more well-versed in the specifics than I.
As for Nova’s list of believers turned skeptics, I’ll defer to Andrew Dessler  and Joe Romm , who have already done such a great job of dismantling Sen. James Inhofe’s list of “400 (or more) skeptics.” For the sake of argument, allow me to highlight just one dubious “quote”: Joanna Simpson’s.
Here’s the excerpt Nova included: “Since I am no longer affiliated with any organization nor receiving any funding, I can speak quite frankly.” Nova goes on to note that Dr. Simpson, an accomplished atmospheric scientist, used to be part of NASA and authored over 190 studies. Fair enough. But is that all she actually said?
If you could have seen her quote in its entirety, this is what you would have read:
“Since I am no longer affiliated with any organization nor receiving any funding, I can speak quite frankly. What should we as a nation do? Decisions have to be made on incomplete information. In this case, we must act on the recommendations of Gore and the IPCC because if we do not reduce emissions of greenhouse gases and the climate models are right, the planet as we know it will in this century become unsustainable. But as a scientist I remain skeptical.”
What a difference a few extra sentences can make.
Read Part One of Debunking the 'Skeptics Handbook': More CO2 Does Worsen Climate Change