I don't know much about meteorites, but here's my evaluation: (Executive Summary: Move along folks, there's nothing to see here.)
What the author did:
He fractured tiny comet-derived meteorites (0.1 - 0.6 g) from two events and examined the freshly broken surfaces. He claims to have observed structures that are remnants of cyanobacteria.
These meteorites are of a special very rare type (only 9 are known). They are about 20% water, and soft enough to cut with a knife. They mainly consist of minerals cemented together with magnesium sulfate ('Epsom salts'). They come from asteroids and comets, not planets like the Alan Hills meteorite from Mars. Hooper's reasoning that they come mainly from comets seems reasonable to me.
They contain quite a bit of organic (carbon-based) material, but I don't know if this differs significantly from the polycyclic aromatic hydrocarbons known to be present in comets. It's true that PAHs found on Earth are usually biological in origin (think of the tarry crud that accumulates on your barbeque grill), but that doesn't mean that PAHs from space have biological origins.
An important concern with this kind of study is contamination with terrestrial organisms before examination. He doesn't say how the meteorites have been stored before he obtained them, nor how the surfaces of the meteorites were treated before being fractured and examined. He doesn't say how they were fractured - might they have been cut with a scalpel blade or just pressed on until they crumbled? He says that the tools were flame-sterilized, but not what the tools were or how they were used.
He used two examination techniques. FESEM is field emission scanning electron microscopy - this seems to be a higher-resolution form of scanning electron microscopy (SEM), with the usual risks of artefacts. The fractured surfaces were not coated with anything before being analyzed - I don't know what effect this might have. The other technique is energy-dispersive X-ray analysis - I gather that this is an add-on to SEM that can scan a specimen and report on the abundance of specific atoms at different positions. Its results can be reported as the distribution of atoms at a particular position or as an image of the specimen, shaded to show the varying density of a particular atom.
He shows an image and analysis of one filament from the Ivuna meteorite. It has more carbon than the surrounding material but no detectable nitrogen or phosphorus.
He bolsters his claim that it's a bacterium by showing an image of the giant bacterium Titanospirillum and an image of another filament from the meteorite. His claim that the sulfur granules in this second filament are like those of Titanospirilum is weakened by the very high sulfur in the surrounding material. And although this filament is similar in size and shape to Titanospirillum (upper images), the other filament is about 15 times smaller (bottom images, adjusted to approximately the same scale).
The image he shows of an inner surface of the Orgueil meteorite has more filaments (no attempt is made at quantitation). These are more complex in structure and fairly similar to each other, suggesting that they were formed by a single kind of process.
The atomic analysis is not at all convincing. He claims that different parts of the filament have different composition, but doesn't present any control analysis of the variability of the measurements or of the background values for positions away from the filaments. He claims that the atom-density scans show enrichment of carbon and oxygen in the filaments, but this looks very weak to me - the only strong signals are for magnesium and sulfur. Again there is no detectable nitrogen or phosphorus.
He spends a lot of text discussing the morpohlogical similarities of these filaments to cyanobacteria, but I don't regard these similarities as worth anything. Filamentous bacteria are very morphologically diverse, and additional variations in appearance are likely to result from inconsistent preparation for electron microscopy. It's probably pretty easy to find a bacterial image that resembles any fibrous structure. In the absence of any statistical evidence to the contrary, it's prudent to assume that such similarities are purely coincidental.
The author tacks on quite a bit of other less-than-compelling information intended to support his claim that life from space is plausible. For example, he shows photos of colonies of coloured microorganisms to support his argument that the colours seen on the surfaces of Europa and Enceladus are biological in origin.
The Ivuna meteorite sample showed a couple of micron-scale squiggles, one of which contained about 2.5-fold more carbon than the background. One of the five Orguil samples had at least one patch of clustered fibers; these contained more sulfur and magnesium than the background, and less silicon. As evidence for life this is pathetic, no better than that presented by McKay's group for the ALH84001 Martian meteorite in 1996.
The Journal and the Editor aren't very impressive either:
The journal proudly announces that it is obtaining and will publish 100 post-publication reviews. But did it bother getting any pre-publication reviews? It will be shutting down in a few months, after only two years of on-line publication (the 13 'volumes' are really just 13 issues). Its presentation standards are pretty bad - there doesn't seem to have been any effort at copy-editing or formatting the text for publication (not even any page numbers).
Chandra Wickramasinghe is the journal's Executive Editor for Astrobiology, and presumably is the Editor responsible for this article. I heard him give a talk pushing panspermia about 10 years ago (the audience was an undergraduate science society at Oxford). The talk was very slick but dreadfully bad as science. The evidence he cited to support his arguments wasn't actually untrue, but he twisted everything to make his arguments seem stronger than they were. He argued like a lawyer - his only goal seemed to be convincing the audience that his conclusion was correct, regardless of the contrary evidence that an unbiased consideration of the evidence would provide. Thus I wouldn't trust his scientific judgment about anything concerning astrobiology.