There are no scientific advances in Western Europe during the early Middle Ages, i.e. between 500AD to 1000AD, just a 'mere' 500+ years... This is actually acknowledged by the writer of the article. Things get somewhat better in the 2nd part of the Middle Ages leading to the Renaissance. So roughly 1000AD-1500AD. The earliest references from the author are in 12th century. Such an intellectually dishonest title.
There's a weird kind of historic revisionism that's been going on the last couple years regarding the Medieval period...the "things weren't all that bad" and "the notion that nothing happened is just a myth". Is it real? Are we just now learning about advanced and invention that happened during this period and were previously ignoring/ignorant of? Maybe. But I suspect something else is at play here, I'm just not sure…
Like a few commenters here, you're confusing the dark ages and the middle ages. You can quibble over semantics and say that the middle ages includes the dark ages, but that obscures the point of the original post.
The standard narrative of Western intellectual progress looks like this:
~300BC to ~400AD: classical civilisation, high intellectual culture
~400AD to ~1500AD: Europe under the dominion of the Church, science and reason suppressed
~1500AD: bam, Renaissance
~1700AD: bam, Enlightenment
~1700AD - present: humanity freed from the yoke of religion, knowledge flowers again.
The revisionist view is as follows:
~300BC to ~400AD: classical civilisation, high intellectual culture
~400AD to ~1000AD: Europe in the dark ages due to barbarian invasions, underpopulated and poor, classical tradition barely kept alive in monasteries
~1000AD to ~1400AD: Europe begins to get wealthier, knowledge flowers in Church-sponsored universities
~1600AD: bam, Protestant Reformation
~1600AD - present: science builds on knowledge and philosophy developed by Catholic church, but Protestant anti-Catholic propaganda creates the false narrative of Church suppression of knowledge.
I don't know why this perspective is hitting the zeitgeist now, but one reason might be that the internet enables niche communities to share such ideas.
One such group is Catholics - here's a Catholic blogger explaining exactly how the heliocentrism vs geocentrism debate played out: http://tofspot.blogspot.com/2013/08/the-great-ptolemaic-smac...
Another group are environmentalists - here's an interesting blogger writing about how classical knowledge was preserved through the dark ages: http://thearchdruidreport.blogspot.com.au/2010/06/merlins-ti...
And a final group are the reactionaries, a group who see the modern ideals of progress as a myth - here's a good starting point on the idea that modern 'progressive' ideas are largely derived from Protestantism: http://unqualifiedreservations.wordpress.com/2007/09/26/how-...
Anyone who's interested and has the free time, please do dig around those blogs - you may realise, as I did, that the 21st century is quite an intellectually narrow and ignorant time.