After atoms formed, the universe entered the 'Dark Ages', when all was dark except for the fading glow of light, shifting constantly toward lower and lower energies. The hydrogen atoms formed when the universe was about 400,000 years old. After that, gravity slowly made dense regions in the universe even denser, until the first galaxies formed, and within them the first sources of light (Read more here about gravity and about the cosmic microwave background). These sources were stars (like our sun) and/or quasars. Quasars are very bright objects seen in the centers of galaxies, and they are thought to almost certainly be massive black holes, with masses between a few million and a few billion times the mass of the sun.

Based on theoretical models, the first galaxies are thought to have formed when the universe was 100-200 million years old. These sources emitted radiation that began to ionize some of the gas in the universe, which had previously been neutral (To ionize a hydrogen atom is to break it apart into an electron and a proton. Read more here about the hydrogen atom and its spectrum). This process is called reionization, where the "re" comes from this entire story: First of all the gas was hot and ionized, then it became cool and neutral, and finally it again became heated and ionized, this time by radiation from stars and quasars. This process was gradual, as more and more galaxies formed, and "complete reionization" refers to the time when all the low-density gas in the universe had been ionized, and only a small fraction of the gas which was in and near galaxies, and very dense, still remained neutral.

In all observations of spectra until the recent ones, all Lyman-alpha absorption was seen to correspond to a small object, either some part of a galaxy, or perhaps the dense gas in a filament which contains a number of galaxies. But every large region seen was transparent (i.e., non-absorbing), implying that the low-density gas (which fills most of the volume of the universe) must be very highly ionized. In fact, James Gunn and Bruce Peterson, back in 1965, showed that the neutral fraction in these regions must be less than one part in 100,000 , otherwise we would have seen large regions with strong absorption. Ever since then, large regions of absorption have been called the "Gunn-Peterson effect". This effect was seen for the first time in the two recent observations. However, this does not mean that the universe was observed in the period before complete reionization. This is because the absorption is very sensitive: Even if the region is highly ionized, so that it only has a neutral fraction of one part in 10,000 , it still produces very strong absorption, and cuts out the spectrum from the quasar over the spectral region corresponding to the location of this gas. Therefore, the recent observations are ambiguous, although what they find is new, and it corresponds at least to a remaining after-effect of reionization, when the gas was ionized but still not very highly ionized.

In a recent paper I found that if we were to observe the universe in the time before complete reionization, we should see very, very wide regions of complete "Gunn-Peterson" absorption (The technical paper is here ). Among the two recent observations, those led by George Djorgovski (at a time which corresponds to a cosmic age of a billion years) found only a relatively small region of absorption, situated between regions where flux is transmitted. Since they did not see a very wide region, this must correspond to the universe after complete reionization (contrary to some of the recent press releases). The other observation (at a cosmic age of 900 million years), led by Robert Becker, actually saw a somewhat longer region of absorption. More importantly, although there was flux seen from regions closer to us, we don't know anything about regions that are more distant: The observed region of absorption extended all the way to the quasar itself. We would need to find a more distant light source in order to probe more distant gas. So it is possible that they saw only a small part of a much larger absorbing region, and that this is a first sign of the universe back when low-density gas was still neutral. But we can't be sure until we actually see much larger absorbing regions.