Mike Flynn Discovers the Dark Ages
(A Rebuttal to Mike Flynn's counter on "The Myth of Christianity Founding Modern Science and Medicine")
by Jim Walker, "the heretic"
Created: Dec. 10, 2009
Additions: 29 Dec. 2009
I recently received an email pointing me to a criticism of my commentary by a Catholic science fiction writer named Mike Flynn. He titles his attack as "The Age of Unreason." I usually don't respond to attacks that include ad hominems, and cheap shots, but he makes some absurd claims and his criticism appears so thorough and condemning that it might seem, to the naive reader, that his assertions are valid. He sure stuck it to me, didn't he? Well, not quite as we shall soon see.
Flynn accuses me as a "freethinker" of getting what you pay for, and nothing in the essay caused him to alter that opinion. He claims I repeat myths and legends, cites no sources, and that I appeal to the ignorance of history and scholarship of the past couple of decades, indeed, of any scholarship at all, etc., etc. We'll see who is spreading the myths here.
Apparently Flynn doesn't realize that I wrote a commentary, not a formal essay, and I didn't feel it necessary to provide full citations anymore than a newspaper op/ed piece. It was directed to Christians who emailed me, making absurd claims about how Christianity founded this or that about science or medicine. I did, however, provide links within the text and sources at the end that are central to the argument. I guess that doesn't count as source material in Flynn's mind.
Ironically, Flynn didn't provide sources in his counter argument. And no, I do not accept his comical list of pictures of books copy & pasted at the end as a valid way to cite source material. How do we know which book he's referring too when he's making claims? Did he actually derive his sources from them or did he just go to Amazon.com and search for books that look like it might impress his readers. I don't know. Lets hope not, because if he did get his sources from them, then the authors of those books got the information wrong, wrong, wrong. This is the world of the internet and Flynn provided no links for his readers to check his sources. They just have to believe that he got his information correct.
Most of Flynn's alleged book sources deal with the Middle Ages, not just to Europe, but to Islam and China as well. These authors concentrate mostly the Upper Middle Ages where the very few innovations occurred. Many of the books don't support his claims or they don't mention science or engineering at all. For example, Toby Huff tries to answer why the Europeans continued to advance science even though medieval Islam and China were more scientifically advanced (my argument!). The real advancement of science, of course, came after the Dark Ages, during the Renaissance and beyond. Pernoud's book does not deal with scientific advancements at all. White's book mostly refers to shock combat, feudalism, chivalry, and the stirrup (which was invented elsewhere, by the way). Ferngren's book deals with science in the Upper Middle Ages through the Renaissance. And on it goes. . .
Of course I am not a Middle Age scholar and I have to rely on the historians and archeologists. If I get the material wrong, then I should make corrections. And, indeed, Flynn did find errors (now corrected). Thanks Mike! For example, I was wrong to cite Vesalius as translating Galen's texts to Latin (but it's interesting that Flynn cites Gerard of Cremona in the 12th century, as the translator, 700 years into the Dark Ages!). However, none of Flynn's criticisms affects the central theme, namely that Christianity does not deserve the credit for founding science or medicine.
I'm not going to address all of Flynn's attacks as most of them are either off topic or just demeaning, but I will address a few.
Flynn writes: "The Romans just weren't interested in science and math, and wrote almost nothing."
Never let the facts get in the way of belief. Indeed it's tragic that there are few surviving Roman writings but if the Romans were not interested in math and science, they couldn't have designed and built those ingenious Roman constructions. You need to calculate dimensions and load capacity to build such impressive structures as the Colosseum, sewer systems, viaducts, ships, etc. Flynn is stuck in Medieval Christendom. Christians know little about Greco-Roman writings because much of the pagan writings were simply ignored. The Christian rage against pagans and Jews, and the destruction of their precious artifacts are summed up by the Catholic writer, James Carroll, as a "pathological culture of holy violence." Some pagan literature, however, did survive. Heron [Hero] of Alexandria was a major contribution to mathematics and he wrote many books. He invented the steam engine, a precision surveying instrument, odometers, a fire fighting water pump, and much more. Much of Hero's writings were destroyed by Christians, but we have a few of his works preserved due to Arab manuscripts. Menelaus of Alexandria was a mathematician and astronomer who wrote several books. The pagan Hypatia was a notable mathematician and philosopher who was deeply interested in science. She wrote several commentaries on mathematics. Alas, the Christians murdered her. Theon, the father of Hypatia was also a scholar, mathematician, and astronomer; and he too died by Christian hands. Pappus, was also considered a great mathematician and wrote several books on mathematics. Claudius Ptolemaeus (Ptolemy), wrote several scientific treatises on astronomy, math and geography. Galen was an accomplished medical researcher of the Roman period. There are numerous other accounts of Roman writings mentioned by contemporary historians but their works are either fragmentary or they no longer exist. Where did they go? So much for Christian preservation of antiquity. The few early Dark Age Christian "mathematicians," however, simply regurgitated what had long been known by the Ancient Greeks, Romans, and Persians (as long as it did not conflict with Church and Bible), and nothing important happened in science and math until centuries later (more on this below).
Then when I put Giordano Bruno in the category of scientist, Flynn disagreed:
Flynn writes: "Bruno was no scientist, but a mystic of the Pythagorean sort."
Well excuse me for accepting historians as describing Bruno as a philosopher, mathematician and astronomer. If Bruno doesn't deserve the title of scientist, then (using Flynn's logic) we should take many off Flynn's list of Middle Age "scientists" who used supernatural nonsense as their modus operandi. For example, Thierry of Chartres tried to explain the creation of the world by basing it on a theological interpretation of Aristotle's four causes, that he identifies with the three persons of the Trinity plus matter etc. John Philoponus also used similar theological reasoning when trying to account for the motion of planets and the creation of the world. By the way, Philoponus' ideas were so unpopular that he appears to have ceased his studies of philosophy and devoted himself to theology instead. After his death, Philoponus was declared to have held heretical views of the Trinity and was made anathema. Oh my.
Moreover, many of those on Flynn's short list were considered scientists, not due to discoveries or for investigative science, but because they studied the works of ancient philosopher "scientists" such as Aristotle and Plato, or mathematics from the the ancient Greeks or Arabs. They should be better called "students of pagan philosophy and math," not scientists. The foundation of science was laid by pagans, not Christians. By the way, Nicholas Cusa doesn't belong in Flynn's list. Cusa lived in the 15th century, not the Dark Ages.
Flynn writes: "Once again, the one and only scientists[sic] ever hassled over a point of natural philosophy is trotted out to do his star turn."
Notice how convenient it is for Flynn to dismiss Giordano Bruno as a scientist so he can reduce the "hassled" scientists to only one. The problem here is that there were few scientists before Bruno and Galileo (both who lived after the Dark Ages, by the way). How does one find scientists to attack when there were so few scientists around? Flynn fails to mention Hypatia, the mathematician, philosopher who was also "hassled" by Christians. Then we have Siger of Brabant, a 13th century philosopher who was summoned, along with Bernier de Nivelles, to appear on a charge of heresy, especially in connection with the Impossibilia, (where the existence of God is discussed). They avoided the charges by fleeing to Italy. Roger Bacon suffered censorship and eventually imprisonment from the Order for the heresy and he died soon after his release from prison. The history of the Dark Ages is filled with censorship and subterfuge. The Catholics in the Dark Ages were the "thought police" of the time.
Flynn then makes one of many unwarranted assumptions about me:
Flynn writes: "Walker does not understand that the Christians believe that God is "existence itself," that he called himself "I AM" . . . . He really ought to disabuse himself of the images of an old man with a long white beard sitting at a drafting table. . . The way to think of creation is not the engineer designing a new species at a cosmic drafting table, but the minnesinger singing a new song."
Flynn goes off topic here, but I just have to respond. Of course I never said or hinted anything about an anthropomorphic god. It always amazes me how some people think they know the mind of other people. Flynn doesn't seem to realize that there are a multitude of Christian beliefs about God. Many people do not believe that God is "existence itself." Some believe that "God is unknowable" and can't be known, even in principle. Some think he is a person they can talk to in the sky that can be pointed to (as do many sport athletes, etc.) Then he goes on to tell others the way to think about creation as a minnesinger singing a new song. What hubris! So much for the "we are the image of God" thing. Fynn's god must not be the Christian God because medieval Christian iconography depicts God as a human being sporting a beard, wearing a robe, whom they call Jesus (incarnatio, or God incarnate). They actually believe he existed. To the Catholics the Trinity represents the central doctrine of their religion where the Godhead consists of three distinct persons. God can even morph into a Ghost!. You can also eat his actual flesh and drink his blood (check out my satire on communion). To put it bluntly, I submit that if you don't believe in an anthropomorphic god, you can't be a Christian because without a human Jesus, well, there goes the New Testament! According to many Christians, Jesus even appears to us on toilet seats, Cheetos, wood grains, wall stains, and even on animal rear ends:
Flynn then attacks the term "Dark Ages":
Flynn writes: "Historians have long ago dropped the silly sobriquet "The Dark Ages," save in part for the actual barbarian Volkerwanderungen."
Silly? Well not to all historians. See this Amazon.com list for examples. Petrarch during the early Renaissance coined the term and I will continue to use it because it fits better than Middle Ages. Why? Because some historians use "Middle Ages" in a generic sense to refer to other non-Christian countries such as China, India, Persia, etc. Also, the Renaissance is considered by some as the "Upper Middle Ages." The Dark Ages is thought of as only referring to Christianized Western Europe, before the Renaissance, thus there is less confusion. I also use it in a similar sense that Petrarch meant as a time of darkness compared to earlier classical antiquity. I encourage others to use the term. It is valid and to the point. Nor is not a term I use to disparage any advancements (the few that they were) that were made during this time but as a comparison to the advances made earlier in history. Apologists always miss that central point.
Nor can anyone blame the Dark Ages on only the Volkerwanderungen outsiders. Once the population becomes dependent on Church and faith, even the barbarians became Christian, and thus, the Christians themselves became the new barbarians. Christians not only attacked each other, they invaded other lands and tried to convert the people to Christianity (sometimes successfully, sometimes not). As John Romer writes, "The Bible that was at the side of Alaric, their greatest warlord. . . the Bible that was carried with the Vandals, as they roamed through France and Spain leaving Gaul 'burning like one great funerary pyre', and it was with them still when they destroyed imperial North Africa." It didn't get better as time went on either. Romer continues, "More heretics and scholars were burned in the Middle Ages than were ever killed in Carolingian times." And lets not forget the first nine Crusades and the other Crusades leading right up to the 15th century. These were, indeed, dark times.
In response to my claims that the priests of Christianity keep the public from education, Flynn responds:
Flynn writes: "The cathedral schools of the early middle ages were open to all."
You forgot about women, Mike, the women. Half the population of Europe! Cathedral schools were mostly oriented around the academic welfare of the noble’s children and girls were excluded from the schools. Although there were a few organized schools for women in convents, girls were generally not taught to read and write unless they had close connections to the Holy Empire. Heretics, pagans, unbelievers, and slaves also did not attend the schools. Slaves were relatively common during the Dark Ages although they declined slowly as serfdom began to spread. Serfdom itself is a form of slavery (the word "serf" traces to the Latin servus, meaning "slave"). These labor peasants were unschooled, and that puts the vast majority of Christians in the Dark Ages as uneducated. Education in the Dark Ages were reserved for the "upper class," namely clergy, knights, lords, and a few of their ladies. And of course you had to be Catholic.
Flynn writes: "Mr. Walker evidently has no idea of the issues of the trial, the particulars of the charges. . . .Galileo was not convicted of heresy, nor was heliocentrism declared heretical. "
Flynn invents another a straw man. I never said anything about conviction; I wrote "imprisoned." Galileo officially surrendered to the Holy Office, and Father Firenzuola informed Galileo that for the duration of the proceedings against him he would be imprisoned in the Inquisition building [source]. Some have tried to argue that this was not imprisonment (being held in a prosecutor's apartment) but anyone who is held against their will is, indeed, imprisoned.
Furthermore, Flynn apparently doesn't understand that claiming evidence for heliocentrism was considered heretical. And spare us the Flynn lecture on Galileo's trial. The information is available in libraries and on the internet. Notice that Flynn provides no links or sources. I implore people to read the actual Papal Condemnation (Sentence) of Galileo themselves instead of invented history from Flynn. The Condemnation includes:
"The proposition that the Sun is the center of the world and does not move from its place is absurd and false philosophically and formally HERETICAL, because it is expressly contrary to Holy Scripture." [bold caps, mine]
"The proposition that the Earth is not the center of the world and immovable but that it moves, and also with a diurnal motion, is equally absurd and false philosophically and theologically considered at least erroneous in faith."
Galileo was ordered to abandon althogether the said false doctrine. He was interrogated with the threat of torture (can you imagine what would have happened to poor Galileo if he refused the order?). To avoid future consequences, Galileo finely wrote a recantation that includes:
". . . after an injunction had been judicially intimated to me by this Holy Office, to the effect that I must altogether abandon the false opinion that the sun is the center of the world and immovable, and that the earth is not the center of the world, and moves, and that I must not hold, defend, or teach in any way whatsoever, verbally or in writing, the said false doctrine, and after it had been notified to me that the said doctrine was contrary to Holy Scripture -- I wrote and printed a book in which I discuss this new doctrine already condemned, and adduce arguments of great cogency in its favor, without presenting any solution of these, and for this reason I have been pronounced by the Holy Office to be vehemently suspected of HERESY, that is to say, of having held and believed that the Sun is the center of the world and immovable, and that the earth is not the center and moves:
Therefore, desiring to remove from the minds of your Eminences, and of all faithful Christians, this vehement suspicion, justly conceived against me, with sincere heart and unfeigned faith I abjure, curse, and detest the aforesaid errors and HERESIES, and generally every other error, HERESY, and sect whatsoever contrary to the said Holy Church, and I swear that in the future I will never again say or assert, verbally or in writing, anything that might furnish occasion for a similar suspicion regarding me; but that should I know any heretic, or person suspected of HERESY, I will denounce him to this Holy Office. . ." [bold caps, mine)
Of course nobody today believes that Galileo denounced heliocentrism in his own mind; we know that he really was a heretic by Papal standards. And even though Galileo fully recanted, he was still committed to house arrest for the rest of his life. And apologists want us to believe this was a time of free inquiry! Fortunately other people knew of Galileo's work, and once his information hit Great Britain, there was not a damn thing the Church could do to stop its spread. This is an example of what I mean by science advancing in spite of religion.
Flynn writes: "Walker also does not understand Aristarchus of Samothrace, the last Librarian of Alexandria. He did not have a heliocentric system."
Flynn's got the wrong Aristarchus. Of course I was referring to Aristarchus of Samos, the first person credited with an explicit argument for heliocentrism. I provided a date (270 BCE). You'd think that Flynn would have checked that out.
Here's another gem:
Flynn writes: "Archimedes did not invent calculus. The method revealed in the lost text was a refinement of the method of exhaustion that he had already written about. You cannot invent calculus using nothing but geometry. You need algebra, and that had not been invented yet."
Historians claim that algebra began in ancient Egypt and Babylon where people learned to solve linear and quadratic equations as well as indeterminate equations. (See History of Algebra) and History). And let's not forget Euclid's Elements (c. 300 BCE) that contains algebra. Archimedes even mentions Euclid in his writings. Nevertheless even without algebra, the Archimedes Palimpsest shows that Archimedes was able to solve problems that are now treated by integral calculus.
It gets worse.
FLYNN UNKNOWINGLY DISCOVERS THE DARK AGE HOLE
And now we get to the meat of the matter. What really caught my eye and served as the prime reason for replying to Flynn's diatribe was his "prima facie" list of alleged scientific and engineering feats allegedly made during the Dark Ages. My original crude graph (shown in my commentary) consisted of only a relational graph. Flynn, however, provides us with science and engineering data points from which we can begin to form a more accurate graph, and from a Catholic apologist to boot! We'll see just who is spreading unwarranted myths around here. Unknowingly, Flynn confirms precisely what I've been saying, and many others before me, in that: science declined during the Dark Ages. Flynn responds with his list of Dark Age achievements:
"In no particular order: watermills, windmills, camshafts, toothed wheels, transmission shafts, mechanical clocks, pendant clocks, eye glasses, four-wheeled wagons, wheeled moldboard plows with shares and coulters, three-field crop rotation, blast furnaces, laws of magnetism, steam blowers, treadles, stirrups, armored cavalry, the elliptical arch, the fraction and arithmetic of fractions, the plus sign, preservation of antiquity, “Gresham’s” law, the mean speed theorem, “Newton’s” first law, distilled liquor, use of letters to indicate quantities in al jabr, discovery of the Canary Islands, the Vivaldi expedition, cranks, overhead springs, latitudo et longitudo, coiled springs, laws of war and non-combatants, modal logic, capital letters and punctuation marks, hydraulic hammers, definition of uniform motion, of uniformly accelerated motion, of instantaneous motion, explanation of the rainbow, counterpoint and harmony, screw-jacks, screw-presses, horse collars, gunpowder and pots de fer, that there may be a vacuum, that there may be other Worlds, that the earth may turn in a diurnal motion, that to overthrow a tyrant is the right of the multitude, the two-masted cog, infinitesimals, open and closed sets, verge-and-foliot escapements, magnetic compasses, portolan charts, the true keel, natural law, human rights, international law, universities, corporations, freedom of inquiry, separation of church and state, “Smith’s” law of marketplaces, fossilization, geological erosion and uplift, anaerobic salting of fatty fish (“pickled herring”), double entry bookkeeping, and... the printing press. (Yeah, some of the innovations are political and economic.) "
This describes a pretty short list considering the Dark Ages lasted for centuries. Moreover, about a quarter of Flynn's claims have nothing at all to do with science or engineering (I suspect these were added in an attempt to pad the list to make it look more impressive). Nevertheless, let's see just how well Flynn's claims stand up. What's wonderful about the internet is that we can search online encyclopedias and books on the fly. I made a few comments and paraphrased somewhat, but mostly I simply lifted and pasted the material directly from the sources. Click on the numbers within the parenthesizes to go to the source material. This is certainly not a thorough study but it makes the point:
watermills: The initial invention of the watermill appears to have occurred in the Hellenized eastern Mediterranean in the wake of the conquests of Alexander the Great and the rise of Hellenistic science and technology. ,  During Hellenistic times, there were even watermills with toothed gears. 
windmills: Hero of Alexandria, a Greek inventor of the third century BCE, once described a small wind-driven "motor" which he had designed to provide air pressure for an organ. An early reference to a wind pump is in a Hindu book written circa 2-4 CE, called Arthasastra of Kantilys , ,  The first definite reference to the use of the windmill came early in the Islamic period.  The first windmills were developed to automate the tasks of grain-grinding and water-pumping and the earliest-known design is the vertical axis system developed in Persia about 500-900 CE. , 
camshafts: The idea of a cam goes back to the first century Greek scientist Hero of Alexandra.  An early cam featuring a camshaft was built into Hellenistic water-driven automata from the 3rd century BCE. 
toothed wheels: The Greek Antikythera mechanism, thought to have been built around 150-100 BCE, contains many metal toothed geared wheels. It is the first known mechanical computer.  Here is a video of a 360 degree virtual representation of the mechanism (click here). Vitruvius (c. 80-70 BCE), describes toothed wheels long before Christianity. , 
transmission shafts: This is a rather generic term as windmills and watermills have transmissions shafts, otherwise they would not be able to transmit its force. A Dragon-Bone waterwheel, for example, invented by Bi Lan in the Eastern Han Dynasty (221-206 BCE) included a transmission shaft.  Su Song's astronomical tower also contained a transmission shaft. 
mechanical clocks: The Chinese invented the first mechanical clock during the Song Dynasty in 1088 CE. European clocks did not appear until about 200-300 years later. 
pendant clocks: I've yet to find the earliest pendant clock during the Dark Ages or elsewhere. I did, however, find mention of pocket sundials (not a particularly impressive engineering claim, however).  This one is pending.
eye glasses: This one is arguable and it depends on what you mean by "eye glasses." Simple class meniscal lenses are mentioned in ancient Egyptian hieroglyphs in the 8th century BCE. Corrective lenses were said to be used by the Arab, Abbas bin Firnas, in the 9th century, who had devised a way to produce very clear glass. The first wearable eye glasses were probably invented at around 1284 by Salvino D'Armate. So I'll give the first "wearable" glasses to the Dark Ages. However, the first practical eyeglasses weren't invented until the 17th century.  Sunglasses date back to ancient China and Rome.  The first optical lens were probably made soon after the art of glass-making was first discovered, prior to 2000BCE. Optical eye lenses date back to a Parthian city (now Baghdad) to about 250-224 BC. Medieval Europe began using "reading stones" (a primitive magnifying glass) at about 1000 CE. 
four-wheeled wagons: The ancient Romans used four-wheeled wagons. According to Dr. Judith Weller, "The wagons built by the Romans were unsurpassed in engineering and technology until well after the Middle Ages. . . . Altogether, a range of vehicles was created in the Roman era which that would satisfy the needs of European society for the next thousand years."  First century BCE Romans even used sprung wagons for overland journeys. With the decline of these civilizations these techniques almost disappeared. ,  During the Hallstatt period (8th to 6th centuries BCE), they used four-wheeled wagons harnessed for two horses.  During king Abargi's time, four-wheeled wagons were used at around 2600 BCE. During the Persian Empire, a four-wheeled carriage called a harmanaxa came into use. 
wheeled moldboard plows with shares and coulters: The first heavy wheeled moulded plow was first developed in Han Dynasty China, around 100 BCE.  The first iron plow was used in the Warring States Period (475-221 BCE) it had a ridge ending in a sharp point (share) with wings (coulter) to throw the soil off the plow.  The historian, Richard Carrier, says the Romans invented the heavy plow. "They had large, wheeled plows that turned the soil, pulled by teams of four to six oxen, already in use by the 1st century A.D. (as described in Pliny the Elder, Natural History 18.48.172-173). The Romans actually had a fairly (and correctly) sophisticated understanding of plow technologies, and kept many different kinds in use, specialized to soil and climate." 
three-field crop rotation: This doesn't really fall under science or engineering. Nevertheless, old crop rotation methods were mentioned in Roman literature, and referred to by several civilizations in Asia and Africa. During the Muslim Agricultural Revolution of the Islamic Golden Age, Muslim engineers and farmers introduced a new modern rotation system where land was cropped four times or more in a two-year period. Three-year rotation wasn't practiced in Europe until from the end of the Middle Ages to the 20th century. 
blast furnaces: The oldest extant blast furnaces were built during the Han Dynasty of China in the 1st century BCE.  Homer describes a blast-furnace with twenty crucibles. 
laws of magnetism: The discovery of magnetism belongs to the Greek scientist Thales of Miletus in the sixth century BCE,  but the first one to describe magnetic laws is debatable. Aristotle attributes the first of what could be called a scientific discussion on magnetism to Thales, who lived from about 625 BCE to about 545 BCE. Around the same time in ancient India, the Indian surgeon, Sushruta, was the first to make use of the magnet for surgical purposes.  Some people seem to think that Pierre de Maricourt in 1269 CE discovered the laws of magnetism. However, according to the Catholic Encyclopedia, Pierre de Maricourt in "part seems to have been, not the discovery of these laws, but their presentation in logical order."  Some attribute William Gilbert as "largely responsible for creating the science of magnetism," but this didn't occur until the 16th century , 
steam blowers: Hero of Alexandria (c. 10-70 CE) gets credit for the first steam engine. Ancient steam-blowers.  Steam-jet- fire-blowers were used in ancient Tibet from which the Middle Age steam blowers probably derived. 
treadles: There is evidence of a treadle-operated spindle-wheel in China during the late Han period (c. 220 CE).  It is also possible that the treadle originated in India, but most authorities establish the invention of the treadle in China.  Ancient China also had a treadle-operated tilt-hammer. 
stirrups: The earliest manifestation of the stirrup was a toe loop that held the big toe and was used in India, possibly as early as 500 BCE. The first dependable representation of a rider with paired stirrups was found in China in a Jin Dynasty tomb of about AD 322. The stirrup appeared to be in widespread use across China by 477 CE. , 
armored cavalry: The ancient Greeks called armored cavalry Kataphraktos (pl. Kataphraktoi) which translated means roughly "covered, protected" or "armored". The term was later borrowed by the Romans (the Latin variant in the Roman Empire being Cataphractarii) and until the Middle Ages in Europe, continued to be used to designate armored cavalry. , 
the elliptical arch: Is this really an engineering advancement? Perhaps it served an aesthetical purpose but not an advancement. Regardless, it appears the Egyptians used elliptical arches.  The semicircular arch was followed in pre-Dark Age Europe by the pointed Gothic arch, whose centerline more closely followed the forces of compression and which was therefore stronger. This design had been used by the Assyrians as early as 722 BCE. 
the fraction and arithmetic of fractions: The early Egyptian and Greeks used fractions long before Christianity. Ordinary fractions without the horizontal bar is due to the Hindus. Several sources attribute the horizontal fraction bar to the Arab, Al-Hassar. 
the plus sign: Hardly a scientific advancement. Although Egyptian hieroglyphics had a symbol for addition, the first known use for the plus sign is found in a book book published by Henricus Grammateus in 1518, during the Renaissance, not during the Dark Ages). 
preservation of antiquity: Preservation of past history was practiced by the early Greeks, Romans, Chinese, Persia, and many other cultures. With the retrenchment of literacy in the Roman west during the fourth and fifth centuries, fewer private libraries were maintained, and those in unfortified villas proved to be among their most combustible contents.  Although there were libraries during the Dark Ages, they were filled mostly by works that did not conflict with Church teachings.
Gresham’s law, the mean speed theorem I don't know why Flynn put Gresham's law with the mean speed theorem but Gresham's law, "Bad money drives out good" was derived by Sir Thomas Gresham in the 16th century.  The mean speed theorem came from Nicole Oresme (also called the Merton theorem) but he lived in the 14th century during the Renaissance, not the Dark Ages.  Sorry.
Newton’s first law: Newton's first law was, of course, derived by Sir Isaac Newton in the 17th century long after the Dark Ages. However, Newton's law is a restatement of what Galileo had already described and Newton gave credit to Galileo. The law of inertia apparently occurred to several different natural philosophers and scientists independently. The inertia of motion was described in the 3rd century BCE by the Chinese philosopher Mo Tzu, and in the 11th century by the Muslim scientists Alhazen and Avicenna.  Mozi, a philosopher who lived in China (470 BCE -390 BCE) composed or collected his thought in the book Mozi, which contains the following sentence: "The cessation of motion is due to the opposing force ... If there is no opposing force ... the motion will never stop." which is, in essence, the same as Newton's law. 
distilled liquor: Early types of distillation were known to the Babylonians in Mesopotamia (in what is now Iraq) from at least the 2nd millennium BCE. Archaeological excavations in northwest Pakistan have yielded evidence that the distillation of alcohol was known in the Indian subcontinent since 500 BCE. Distillation was later known to Hellenistic alchemists from the 1st century CE. 
use of letters to indicate quantities in al jabr: I don't know what Flynn means to here unless al jabber refers to an Arabic word referred to by the Arab mathematician Mohammed ibn-Musa al-Khowarizm.  What this has to do with an invention from the European Dark Ages, I haven't a clue.
discovery of the Canary Islands: This is neither science or engineering, however, King Juba, Augustus's Roman protege, is credited with discovering the islands for the Western world, and he dispatched a contingent to re-open the dye production facility at Mogador in the early 1st century CE. 
the Vivaldi expedition: This is also not science or engineering. Vivaldi and the Vandino brothers sailed along the coast of present-day Morocco after passing the straits of Gilbraltar. They may have followed the African coast as far as Cape Non. Their subsequent fate is unknown. I hardly doubt that they were the first sailors who sailed along the coast of Morocco and Africa. 
cranks: In China, hand-operated cranks appeared during the Han Dynasty (202 BCE-220 CE). They also appeared in 5th century BCE Celtiberian Spain and ultimately spread across the Roman Empire. ,  Also, the 3rd century Roman Hierapolis sawmill contained a crank and connecting rod mechanism. 
overhead springs: I'm not sure what Flynn means by "overhead" here but springs have been used long before Christianity. Leaf springs were used on the Tutankhamum-class chariot at around 1333 BCE. The Roman Empire used leaf springs on two-wheeled vehicles called a Pilentum.  The replacement of the flexible bow by the torsion spring gave a great boost to catapult engineering a half century after the invention of the catapult.  Note, the first catapults appeared around 400 BCE. 
latitudo et longitude: The used of grid lines (latitude and longitude) was first suggested by the Greek astronomer Hipparcus about 300 BCE. Shortly after, Hipparcus devised the method of fixing the location of places on earth by observation of the celestial bodies--the sun, moon and stars. He worked out the mathematics of spherical trigonometry, which allowed the results of these observations to be plotted on an earth that he perceived to be a sphere. Some 75 years later (around 225 B.C.) Eratosthenes, another Greek mathematician and astronomer, measured the circumference of the earth (accurate to within 300 miles) raising the art of mapmaking to new standards of accuracy. From that point on, the Greeks could find latitude quite easily. They knew the position of the sun north or south of the equator. By using spherical trigonometry they could measure the sun's angle at noon relative to the equator. Noon was easy to determine since it occurred when the sun was at its highest point in the heavens.  Claudius Ptolemy (90–168 CE) thought that, with the aid of astronomy and mathematics, the earth could be mapped very accurately. Ptolemy revolutionized the depiction of the spherical earth on a map by using perspective projection, and suggested precise methods for fixing the position of geographic features on its surface using a coordinate system with parallels of latitude and meridians of longitude. 
coiled springs: Coiled springs were not invented during the Dark Ages. Henry De Vick had a primitive clock that used a coiled spring but that was in 1379 during the Renaissance.  Some claim they first appeared later in the 15th century 
laws of war and non-combatants: This has nothing to do with science and engineering but considering the crusades and wars throughout the Dark Ages and the vast killing of innocent people, this hardly stands as something to boast about. Nevertheless, according to "A Brief History of the Laws of War, "Attempts to put limits on wartime behavior have been around since the beginning of recorded history and there have been numerous attempts to codify the rules of appropriate military conduct. In the sixth century BCE, Chinese warrior Sun Tzu suggested putting limits on the way that wars were conducted. Around 200 BCE, the notion of war crimes as such appeared in the Hindu code of Manu." 
modal logic: Although Aristotle's logic is almost entirely concerned with the theory of the categorical syllogism, there are passages in his work, such as the famous sea-battle argument in De Interpretatione, that are now seen as anticipations of modal logic and its connection with potentiality and time. Modal logic as a self-aware subject owes much to the writings of the Scholastics, in particular William of Ockham and John Duns Scotus, who reasoned informally in a modal manner, mainly to analyze statements about essence and accident. However, formal workable modal logic didn't exist until 1910. C.I. Lewis is credited for founding modal logic. , 
capital letters and punctuation marks: This has nothing to do with science and engineering. Regardless, the oldest known document using punctuation is the Mesha Stele (9th century BCE). The ancient Greeks and Romans also used forms of punctuation.  Capital and small letters are differentiated in the Roman, Greek, Cyrillic and Armenian alphabets. European languages did not make this distinction before about 1300; both majuscule and minuscule letters existed, but a given text would use either one or the other. 
hydraulic hammers: According to the documentary "Ancient Discoveries", "One thousand years ago, when Europe was still in the dark ages, China was at the forefront of technology. We unveil the remarkable story of how China created a myriad of ingenious devices including cosmic machines able to collect data on the stars, hydraulic hammers. . ."
definition of uniform motion: I can find no reference to a mathematical definition of uniform motion during the Dark Ages. Galileo, however, did describe in his principle of relativity, that all uniform motion is relative, but this was after the Dark Ages. 
uniformly accelerated motion: Again this was described by Galileo well after the Dark Ages, however, the science of kinematics (the description of the motion of objects) dates back to the ancient Greeks. , 
instantaneous motion: Aristotle and Zeno argued about instantaneous motion. However, Roger Bacon in the 13th century tried to distinguish between motions in a void that were instantaneous and those that were successive. ,  These "instantaneous" contemplations were more metaphysical arguments than they were of any practical matter, however.
explanation of the rainbow: Christian Europeans were not the first to describe an explanation of rainbows. In Song Dynasty China (960–1279 CE), a polymathic scholar-official named Shen Kuo (1031–1095) hypothesized—as a certain Sun Sikong (1015–1076) did before him—that rainbows were formed by a phenomenon of sunlight encountering droplets of rain in the air. Paul Dong writes that Shen's explanation of the rainbow as a phenomenon of atmospheric refraction "is basically in accord with modern scientific principles. The Persian astronomer, Qutb al-Din al-Shirazi (1236–1311 CE), gave a fairly accurate explanation for the rainbow phenomenon. This was elaborated on by his student, Kamal al-Din al-Faris (1260–1320 CE), who gave a more mathematically satisfactory explanation of the rainbow. 
counterpoint and harmony: This has little to do with science and engineering, however, Pythagoras (or his followers) developed musical theory including harmonic ratios.  Counterpoint wasn't really elaborated until the Renaissance. 
screw-jacks: Tapered wood-screws appeared in Gallo-Roman times but Villard de Honnecourt in the 13th century apparently is the first to describe a screw jack for lifting loads.  However, it is not known if one was actually built. Nevertheless, I will give this, tentatively, to the Dark Ages. I say tentatively because it is hard to accept that the Romans who used screw presses (see below) would not have thought to modify them for lifting heavy objects. Further research is needed here.
screw-presses: Heron of Alexandria describes a screw press (also called the "Greek press") but it was common enough in Rome in the days of Vitruv (25 BCE). The application of the screw as a source of direct pressure on the mass is a very important step taken at Rome about 50 CE., according to Pliny. , 
horse collars: Throat-birth harnesses could be found in many ancient civilizations. This type of collar was known in ancient Chaldea (3rd millennium BCE), both Sumeria and Assyria (1400 BCE–800 BCE), New Kingdom Egypt (1570–1070 BCE), Shang Dynasty China (1600 BCE–1050 BCE), Minoan Crete (2700–1450 BCE), Classical Greece (550–323 BCE), and ancient Rome (510 BCE–476 CE). With this ancient harness, ploughs and carts were pulled using harnesses that had flat straps across the neck and chest of the animal, with the load attached at the top of the collar, above the neck, in a manner similar to a yoke. The throat-girth design was not improved until the Chinese breast-strap or "breastcollar" harness developed during the Warring States (481–221 BCE) era in China. The fully developed collar harness was developed in Southern and Northern Dynasties China during the 5th century CE.The horse collar eventually spread to Europe circa 920 CE. 
gunpowder and pots de fer: Gunpowder is regarded as being invented, documented and used in China where the Chinese used gunpowder and bombs against the Mongols when they invaded on top of city fortifications. A "pots de fer" is a type of primitive cannon used during the Dark Ages. The earliest known cannon was invented by Ctesibius of Alexandria, in the 3rd century BCE. However, cannons were first used in China, they were among the earliest forms of gunpowder artillery, and over time replaced siege engines—among other forms of aging weaponry—on the battlefield. 
that there may be a vacuum: Aristotelian doctrine did not accept the vacuum and since so much of Catholic philosophy was based on Aristotle, the belief against a vacuum continued during the Dark Ages. The Roman philosopher and poet, Lucretius (c. 94-50 BCE), however, disagreed with Aristotle and speculated about atoms and the void long before medieval times. . In the 13th century, Tempier hypothesized about a vacuum, but it was not on scientific grounds, but rather on supernatural beliefs. "When Tempier declared that the omnipotent God could create a vacuum if he so desired, Tempier insisted that God could break any Aristotelian law." This kind of thinking is not only unscientific but it represents a similar kind of belief (like dogmatically believing Aristotle) that prevented Christians from thinking about a vacuum in the first place. Despite Templier's hypothesis, Christians continued to believe Aristotle's doctrine that "nature abhors a vacuum." It took until the 17th century for Torricelli and Pascal to demonstrate by experiment that nature can have a vacuum. , 
that there may be other Worlds: This is not science but imagination. Tempier in the 13th century did hypothesize about other worlds, but, again, based his idea on religious nonsense as he insisted that God could create life on other worlds if he wished. Christians want us to believe that Tempier's stress on God's omnipotence opened up all kinds of possibilities for the understanding of the cosmos, but it came from such religious beliefs in the first place that barred people from thinking about it. This is like the guy beating his head against the wall only to discover that if he stops beating his head, he will feel better. If people had no head beating dogmatic beliefs in the first place, there would be no such barrier to questioning any possibility, scientific or not.
Nor was any Christian the first to imagine other worlds. Lucian of Aamosta (125-180 CE) anticipated "modern" fictional themes like voyages to the moon and Venus, extraterrestrial life and wars between planets centuries before Jules Verne and H. G. Wells. His novel is widely regarded as an early, if not the earliest science fiction work. 
that the earth may turn in a diurnal motion: It should be remembered that during the Christian Supreme Inquisition in the 17th century against Galileo Galilei they denounced Earth's diurnal motion. Here is an excerpt from the Inquisition:
"That the Sun is the centre of the universe and doth not move from his place is a proposition absurd and false in philosophy, and formerly heretical; being expressly contrary to Holy Writ: That the Earth is not the centre of the universe nor immoveable, but that it moves, even with a diurnal motion, is likewise a proposition absurd and false in philosophy, and considered in theology ad minus erroneous in faith…" 
It is precisely this kind of religious nonsense that held science back for centuries to begin with.
that to overthrow a tyrant is the right of the multitude: This sounds very much like The Twelve Articles of the Black Forest, written during the Renaissance. If so Flynn forgot to include the right to remove a preacher. (see human rights below). This has nothing to do with science and engineering, however, if believed, then why-oh-why didn't the multitude throw out the priestly and kingly tyrants during the Holy Dark Ages?
the two-masted cog: Cogs are a type of small primate cargo ship that first appeared around the 12th century. It's hardly something to brag about especially considering that the Ancient Greeks around 400 BCE had wooden ships weighing about 150 tons and later in 240 BCE, boats were weighing 350 to 500 tons. Ships began adding sails with the increase in size. Two to three masts were common. Some cargo ships were called trading ships or haulers. These ships had very deep hulls and broad beams (width), which helped them sail close to the wind.  In the Tomb of the Ship in Tarquinia, there is a depiction of an Etruscan merchant ship with two masted sails.  By at least the fifth century BCE, merchant ships of 400 ton capacity were carrying the large bulk cargoes in the Mediterranean. Modern merchant ships larger than this were not built until the nineteenth century AD. The largest known merchant ship of ancient times was built for Hiero II, king of Syracuse 270-215 BCE, to carry grain from Egypt. It carried three masts and required a bilge pump designed by the famous ancient engineer Archimedes. The cargo on its maiden voyage included 60,000 measures of grain, 10,000 jars of preserved Sicilian fish, 20,000 talents of wood, and 20,000 talents of miscellaneous goods. This cargo weighed 2000 tons by modern estimates. In the event that the king wished to accompany a voyage, the ship was also equipped with luxury accommodations, including cabins with mosaic floors, promenades decorated with plants, a gymnasium, a bath room fitted with copper tubs and marble basins, a library, and a chapel to Aphrodite. 
infinitesimals: The notion of infinitesimally small quantities was discussed by the Eleatic School. Archimedes, in "The Method of Mechanical Theorems," was the first to propose a logically rigorous definition of infinitesimals. The Iraqi mathematician, Alhazen (965-1039 CE), wrote a number of treatises on infinitesimal mathematics, nine of which have survived.  Infinitesimal calculus was independently invented by both Leibniz and Newton in the 1660s. 
open and closed sets: I can't find any reference to set theory before George Cantor and Richard Dedekind in the 1870s. Since a formal understanding of sets wasn't established until Cantor, It's difficult that someone in the Dark Ages, even if he mentioned sets, had a useful construction of this theory before Cantor. I could be wrong.
verge-and-foliot escapements: The earliest liquid-driven escapement was described by the Greek engineer Philo of Byzantium (3rd century BCE) in his technical treatise Pneumatics. In China, the Tang Dynasty Buddhist monk Yi Xing along with government official Liang Lingzan applied the escapement in 723 (or 725) to the workings of a water-powered armillary sphere and clock drive. However, the first crude verge escapement was used in a bell ringing apparatus called an alarum for several centuries before it was adapted to clocks. In 14th century Europe it appeared as the timekeeper in the first mechanical clocks, which were large tower clocks. Its origin is unknown, and even when it was first used, because it is difficult to distinguish which of these early tower clocks were mechanical, and which were water clocks. However, indirect evidence, such as a sudden increase in cost and construction of clocks, points to the late 13th century as the most likely date for the development of the modern clock escapement.  It should also be noted that the verge is the most inaccurate of the widely-used escapements. The increase in accuracy of clocks didn't occur until the mid 1600s with the invention of the pendulum and balance spring. 
magnetic compasses: The magnetic compass is an old Chinese invention, probably first made in China during the Qin dynasty (221-206 BCE). Magnetized needles used as direction pointers instead of the spoon-shaped lodestones appeared in the 8th century AD, again in China, and between 850 and 1050 they seem to have become common as navigational devices on ships. The first person recorded to have used the compass as a navigational aid was Zheng He (1371-1435 CE), from the Yunnan province in China, who made seven ocean voyages between 1405 and 1433. , 
portolan charts: Portolan comes from the Italian adjective portolano, meaning "related to ports or harbors."  These primitive charts simply showed harbors and trade routes along the coast. Humans have been using maps for navigation for up to 8000 years ago. Scylax, a sailor who lived around 515 BCE made a record of his Mediterranean voyages in c. 515 BCE. This is the earliest known set of Greek periploi, or sailing instructions, which became the basis for many future mapmakers, especially in the medieval period.  (Periploi are documents that listed, in order, the ports and costal landmarks. ) Claudius Ptolemy (90–168 CE) thought that, with the aid of astronomy and mathematics, the earth could be mapped very accurately. Ptolemy revolutionized the depiction of the spherical earth on a map by using perspective projection, and suggested precise methods for fixing the position of geographic features on its surface using a coordinate system with parallels of latitude and meridians of longitude.  Ptolemy's eight-volume atlas Geographia is a prototype of modern mapping and GIS. It included an index of place-names, with the latitude and longitude of each place to guide the search, scale, conventional signs with legends, and the practice of orienting maps so that north is at the top and east to the right of the map—a universal custom today.
Early forms of cartography in India made detailed maps of considerable length describing the locations of settlements, sea shores, rivers, and mountains. Muhammad ibn Musa al-Khwarizmi's "Book on the appearance of the Earth" was completed in 833. It is a revised and completed version of Ptolemy's Geography, consisting of a list of 2402 coordinates of cities and other geographical features. , 
the true keel: The backbone of many ships even dating back to the ancient Egyptians included a longitudinal bottom keel that extended from bow to stem. Aren't those true keels?  However, I did find one reference to that term In "London In Roman Times London Museum Catalogues No. 3".  It describes a Roman ship with a true keel. Roman London, by the way covers a period from around 47 CE. , I also found reference to Viking ships having true keels , , .
natural law: Socrates and his philosophic heirs, Plato and Aristotle, posited the existence of natural justice or natural right. Of these, Aristotle is often said to be the father of natural law. Aristotle's association with natural law is due largely to the interpretation given to his works by Thomas Aquinas. This was based on Aquinas's conflation of natural law and natural right, the latter of which Aristotle posits in Book V of the Nicomachean Ethics (Book IV of the Eudemian Ethics). 
human rights: Human rights? Like human rights for slaves and serfs? Do you mean the inquisitions, pogroms and massive violent attacks against Jews and pagans, burning heretics, the crusades against Muslims, the selling of indulgences? So much for Dark Age human rights. Again this has nothing to do with science or engineering but the concept of rights existed in pre-modern cultures; ancient philosophers such as Aristotle wrote extensively on the rights (to dikaion in ancient Greek, roughly a "just claim") of citizens to property and participation in public affairs. However, neither the Greeks nor the Romans had any concept of universal human rights; slavery, for instance, was justified both in classical and medieval times as a natural condition.
Some people think that the first record of human rights in Europe are from the The Twelve Articles of the Black Forest, in 1525 CE. (during the peasant uprising in the Renaissance period). This is interesting because the Renaissance largely resulted from the populace beginning to reject religious authority. Among the Twelve Articles includes rights such as: "Every municipality shall have the right to elect and remove a preacher if he behaves improperly" and, "The preachers shall be paid from the great tithe. A potential surplus shall be used to pay for the poor and the war tax." If preachers and priests behaved properly, in the first place, there would have been little need for the Articles.  Martin Luther responded with his "Against the Murderous, Thieving Hordes of Peasants," one of the most cruel documents ever written that called for the peasants' destruction.  Stephen J. Gould writes that "the victorious nobility followed Luther's recommendation, and estimates of the death toll (mostly inflicted upon rebels who had already surrendered and therefore posed no immediate threat) run as high as 100,000."  The Twelve Articles were yet another example of (an attempt of) progress "in spite of Christianity."
international law: Do you mean laws that allowed Christians to determine the fate of pagan civilizations through war or to force convert them to Christianity? This is nether science nor engineering but the ancient Greeks before Alexander the Great formed many small states that constantly interacted. In peace and in war, and inter-state culture evolved that prescribed certain rules for how these states would interact. These rules did not apply to interactions with non-Greek states, but among themselves the Greek inter-state community resembled in some respects the modern international community. 
universities: Precursors of the university occurred in ancient Greece at the University of Athens, founded by Plato. It was from the Greeks that the Dark Age teachers got most of their sources. In China the Nanjing University was founded in 258 CE. In Korea, Taehak was founded in 372 CE and Gukhak was established in 682 CE. In India, the Nalanda University was established in the 5th century CE. In Iran the Academy of Gundishapur was an important medical center of the 6th, 7th and 7th centuries CE. In Japan Ashikaga Gakko was founded in the 9th century.
If the definition of a university is assumed to mean an institution of higher education and research which issues academic degrees at all levels (bachelor, master and doctorate) like in the modern sense of the word, then the medieval Madrasahs, or more specifically the Jami'ah, founded in the 9th century would be the first examples of such an institution.
The Gupta rulers in India encouraged higher learning by patronizing centers of higher education at Nalanda, Takshila, Ujjain, Vikramshila and Vallabhi. Each university specialized in a particular field of study. Takshila specialized in the study of medicine, while Ujjain laid emphasis on astronomy. Nalanda, being the biggest center, handled all branches of knowledge. During the Gupta period India became a center for higher studies by attracting scholars from all parts of India and from several foreign countries. These universities became popular in the seventh and eighth centuries A.D. People flocked to the Sarnath university to study Buddhist religion and to Ajanta to specialize in art, architecture and painting. These educational institutions were financed by grants of land and liberal donations from kings as well as from other affluent people.  The first university in the Europe didn't appear until almost 700 years after the beginning of the Dark Ages! 
corporations: Entities which carried on business and were the subjects of legal rights were found in ancient Rome, and the Maurya Empire in ancient India.  The Romans developed a number of forms of organizations that were similar in many ways to the corporation. Roman municipal organizations gradually assumed duties in public affairs and engaged in activities that required the ownership of property. The organizations possessed a number of the attributes of corporations, including continuous existence regardless of changes in membership. the subject of debate. Some authorities profess to see in the group character of primitive societies the fundamental notion of a corporate whole existing even before the individual was regarded as a distinct entity. 
freedom of inquiry: Do you mean like openly inquiring about the non-existence of God, or openly practicing alchemy or science that contradicts Church dogma? Or how about inquiring about sexuality or freedom or to do as one pleases as long as it hurts no one? Does this mean freely practicing another religion besides Christianity? Any civilization that does not allow these things, does not deserve credit for freedom of inquiry, sorry.
separation of church and state: What?! For centuries during the Dark Ages monarchs ruled by the idea of divine right, which said the king ruled both Crown and Church, a theory known as caesaropapism. On the other side was the belief that the Pope, as vicar of God on earth, should have the ultimate authority over the state. Moreover, throughout the Middle Ages the Pope claimed the right to depose the Catholic kings of Western Europe and tried to exercise it. ,  The Gregorian Reform (c. 1050-1080 CE) by Pope Gregory VII made it perfectly clear about the union of church and state. It was based on his conviction that the Church was founded by God and entrusted with the task of embracing all mankind in a single society in which divine will is the only law; that, in her capacity as a divine institution, she is supreme over all human structures, especially the secular state; and that the pope, in his role as head of the Church under the petrine commission, is the vice-regent of God on earth, so that disobedience to him implies disobedience to God: or, in other words, a defection from Christianity. He acknowledged the existence of the state as a dispensation of Providence, described the coexistence of church and state as a divine ordinance, and emphasized the necessity of union between the sacerdotium and the imperium. At no period would he have dreamed of putting the two powers on an equal footing; the superiority of church to state was to him a fact which admitted of no discussion and which he had never doubted.  This is about as far as one can get from separation of church and state.
“Smith’s” law of marketplaces: I'm not sure which Smith Flynn is referring to here. If he's referring to Adam Smith, he certainly had something to say about free market economics but he lived in the 18th century. Moreover, it has nothing to do with science or engineering.
fossilization: There are references to "dragon" bones found in China 2000 years ago but they probably did not deduce them as ancient.  Xenophanes (570-480 BC) wrote about fossil sea shells indicating that land was once under water. During the Middle Ages, fossils were discussed by the Persian naturalist, Ibn Sina (known as Avicenna in Europe) but he was not a Christian. In early modern Europe, the systematic study of fossils emerged as an integral part of the changes in natural philosophy that occurred during the Age of Reason. The nature of fossils and their relationship to life in the past became better understood during the 17th and 18th centuries, and at the end of the 18th century the work of Georges Cuvier ended a long running debate about the reality of extinction and led to the emergence of paleontology, in association with comparative anatomy, as a scientific discipline. 
geological erosion and uplift: Shen Kuo (1031-1095 CE) in China is one of the first naturalists to have formulated a theory of geomorphology. This was based on his observations of sedimentary uplift, soil erosion, deposition of silt, and marine fossils found in the Taihang Mountains. It wasn't really until the 17th century that geology made great strides in its development.  However, because of trying to prove the Bible's authenticity such as the Great Flood and the age of the Earth, geology was held back until much later. Unfortunately many Christian young earth creationists still don't accept the science of modern geology.
anaerobic salting of fatty fish (“pickled herring”): Does this, arguably unhealthy, food preparation even deserve mentioning? Nevertheless, Robert I. Curtis in "Salted Fish Products in Ancient Medicine" reports Galen as describing a piquant fish sauce, would create 'a very pleasant and useful medicine and food'. . . . This dual purpose of fish sauces and other salted fish products, that is a food and medicine, established for them an important place in Greek and Roman social and economic life."  Tonnes Bekker-Nielson's "Ancient fishing and fish processing in the Black Sea region" says, "Our literary sources testify to the widespread culinary and medicinal use of salted fish and fermented fish sauces in antiquity, and especially in the first centuries CE." 
double entry bookkeeping: The origins of a primitive double-entry system may possibly be traced as far back as the Roman Empire. Later there are traces of the double-entry system in the accounting of the Islamic world from at least the 12th century. The earliest record of Dark Age double-entry form didn't occur until end of the 13th century. 
printing press: The printing press is not an invention of the Dark Ages. Woodblock printing was invented by the Chinese to a date before 220 CE and from Egypt to the 4th century. The first printing press was invented in China by 593 CE and the first printed newspaper was available in Beijing in 714 CE. Block printing was developed in Arabic Egypt during the 9th-10th centuries. Movable type printing appeared in China around 1040 CE. Later a more complex system of revolving tables and number association with written Chinese characters appeared by 1298 CE. In Christian Europe, the printing press didn't exist until Gutenberg made one at about 1436 CE, during the Renaissance. , , 
It's also noteworthy that Gutenberg's press was a secular private endeavor not financed by the Church or a ruler. Although the first use of Gutenberg's press was used for religious propaganda, and Bibles, (which only continued to spread supernatural nonsense and church dogma) it also was used for secular and scientific papers which further reduced religious influence in Europe. During the Enlightenment, secular books far outnumbered religious tomes. Thus religion became diluted and the Church no longer had power to hold back scientific progress.  Another example of progress "in spite of Christianity."
In summary, of Flynn's science and engineering claims, how many can be attrubuted to the Dark Ages? Three or possibly four.
1. eyeglasses, 1284 CE (the wearable kind)
2. screw-jacks, 1230 CE (although I suspect the ancient Romans had screw lifting devices, but I haven't yet found a source.)
3. verge and foliot mechanism (but more likely invented in the 14th century)
Possible inventions: pendent clocks (but I could find no information about them).
It's also revealing to note that even these few Christian "achivements" occurred only during the later period of the Dark Ages.
Once you put Flynn's data point into a timeline, the "hole" becomes even more striking. Almost all of Flynn's claims falls before, or after the Dark Ages (or beside from other non-Christians) and we can see the Christian Dark Age hole appearing:
It's like someone boasting about his skill at darts but when he throws, he not only misses the center, but the majority of darts miss the entire dartboard!
Note, I used only Flynn's alleged science and engineering claims for the data points, not the political stuff (which were also not Dark Age originals).
Of course I don't, for one moment, think that this represents a complete list of Dark Age inventions. There are also minor inventions such as those ugly flying buttresses designed to make larger cathedrals to persuade people to hold supernatural beliefs. Then there are the weapons of war (flail, Falchion sword, etc., (none of which play any importance today). The Guillotine was invented during the Dark Ages, called the Gibbet (no it wasn't invented during the French Revolution). Then there were the clever instruments of torture that never appear on the apologists lists. Of course the Greeks and Romans had their torture devices, but the Christians in the Dark Ages (and centuries after) took it to a whole new level such as the Rack, the Pear of Anguish, the Breast Ripper, the Head Crusher, the Saw Torture, the Spanish Tickler, Garrotte Torture, the Wheel Torture, Foot Roasting stocks, Thumbscrew Torture, the Heretics Fork, the Lead Sprinkler, the Knee Splitter, the Spanish Spider, Pillory Torture, the Crocodile Tube, the Brank, the Copper Boot, the Pendulum, etc. Flynn wants us to believe that the Middle Ages were a time for free inquiry. Yes there was some intellectual freedom for priests and the elite but I shudder to think what would happen to a freethinker living during the Dark Ages.
If you add the many other accomplishments made by the Greeks, Romans, China, Persia, etc., the Hole of the Dark Ages become even more revealing. In fact it becomes devastating by comparison. I don't have the time or wherewithal to collect all the data but this would be an interesting study by scholars to put together the compiled data into a visual representation for all to see.
As you can see, Mike Flynn has done nothing but what Catholics have done for centuries: spreading propaganda. The word itself is a Catholic invention derived from Congregatio de Propaganda Fide, "Congregation for Propagating the Faith," established by a committee of cardinals under Pope Gregory XV.
In the end, the only thing Flynn proves is that some people still live in the Dark Ages.
A Note about the age periods: Historians have tried to pin down the periods for the ages, but these are arbitrary. Historians roughly place the Dark Ages between the fall of Rome and the beginning of the Renaissance. The Middle Ages are roughly the same period but others include the Renaissance as the "upper Middle Ages." Some (as I do) put the Dark Ages as starting with the Death of Hypatia because this is approximately where the practice of paganism ended in Europe. Some refer to a Renaissance of the 12th century. Art historians sometimes place the end of the Renaissance at the beginning of the16th century, other historians put its end at the beginning of the Enlightenment age. Confusing isn't it? If you don't like the term Dark Ages or Renaissance, it changes nothing; simply refer to the dates.
Also see Richard Carrier's blog post on "Flynn's Pile of Boners"
Antikythera Mechanism - Part 1, Part 2
The Genius of Archimedes
Rome: Engineering An Empire - Behind the Scenes
Ancient Rome in Google Earth
Religious War on Science: Giordano Bruno
Roman Roads and Bridges
Heron of Alexandria