Interesting opening. Although I'll get to the specifics of your posts, I want to start with a brief overview of some things that have happened so far:
1: Aside from argument 2, Flint's reasons why leaving the stone age is good assumes a value system in which humans are a priori. That doesn't work: if I win a risk of even a single one of my scenarios being true, it means humans should not be valued because either:
A: They will inevitably destroy themselves, or
B: The advancement of humans comes at the expense of other creatures and habitats, in addition to habitats upon which humanity depends.
To that end, if I win this argument, the evaluation of what is "good" is far from conventional wisdom. You should evaluate the debate not based on who saves the most humans, but on who keeps humans down the most before we can bring the planet and possibly bodies outside the Earth down in a fiery blaze.
2: Flint has absolutely 0 answer to a couple scenarios. Most notably, he skipped the quantum vacuum mining scenario. Don't let him write new answers to these for the following reasons:
A: There were no time restrictions on posting. He had plenty of time to write his arguments.
B: I didn't post this response for two days, giving him a ton of time to look back and edit.
C: I had all my arguments perfectly numbered. There's no reason he should have missed argument 2, while answering arguments 1 and 3.
D: Allowing new answers would degrade the debate to the question of who can sneak in the most new stuff later in the debate, killing any capability to discuss the topic.
E: The strategy behind what I did during this post was based on the strategic choices Flint decided to make. Don't punish me for his failure in this regard.
This should be considered a conceded argument, thus meaning that, within this context, we should assume a 100% risk that humans will inevitably destroy themselves, and the universe, through attempts at mining the quantum vacuum.
3: Flint provides no reason as to why humans prevent any extinction-level events at the astronomical scale. That means that, even if I concede 100% of his opening statements, the best you can hope for in preserving human technological advancement is to preserve life on Earth. In contrast, my arguments indicate that human existence has a risk not only of destroying our planet, but of destroying much more. A simple utilitarian calculus would tell you that, all other things being equal, it's preferrable to sacrifice a single species, or even the planet, to save a universe.
Now to his opening statement
1: Humanity's extinction.
General answers
A: I can concede these scenarios, and it only helps out my case. My opening was an indictment of humanity. If I win a risk even one scenario, it means human extinction is inevitable. Furthermore, destroying humanity due to a plague, starvation, or another calamity would prevent them from ever building tools like monocropping or artificial intelligence, which extend the destruction far beyond the human species. This was NOT the best argument to write against me.
B: Isolation of communities prevents your global calamities. Just as smallpox never reached Native Americans until Europe landed, so too would calamities be isolated to specific regions.
Now to the specifics
A: Disease
1: Native Americans empirically prove you wrong, in that they existed for many millenia without being wiped out, and only were wiped out after the intervention of post-stone age humans.
2: How many easily transmissible diseases have a 100% kill ratio?
B: Food supplies
1: Native Americans prove you wrong on this question. There's plenty of food to sustain humans. It's only a question of how many people there are per square mile. We need agriculture to sustain huge populations condensed into small regions (cities).
2: If I win monocropping below, it's another reason why this argument is bad.
C: Weather
1: We can't change the weather. The best you can do is adaptation.
2: The fact that pre-industrial humans lived through the ice age, the transition from the ice age, and the mini ice age (not using Europe as my example: only Native Americans, which were pretty much the only tribe with ancient technology levels still living during the mini ice age) proves you wrong.
3: Aside from global weather calamities, extinction-level events won't result in human extinction, simply because they don't have expanded global implications. The probability of these scenarios, therefore, is slim.
D: Interbreeding
communities interact with one another, allowing the exchanges of genetic material among them.
Now to your argument 2
First, let me start with one thing: Don't worry, Flint, I'm not going to base any of my argument on whether global warming is real. We can just stay away from that debate entirely. 
That being said, group both A and B here.
1: Your examples of protecting other things are defensive protection mechanisms. That is, humanity began making moves which hurt the proliferation of these species, then established your proposals to reverse trends caused by humanity.
Hypothetical example: The Zarf Beetle has a population of 1 million bettles throughout the continent of Politica. Then humans began industrializing the land, cutting down the population of Zarf Beetles to 10,000. A conservation effort was thus put into place to repopulate the beetle, and successfully brought the population to 900,000 bettles.
In this example, do humans get credit as preserving nature? Nope.
A: The ecosystem proved that it could sustain 1 million Zarf Beetles without human assistance. Thus, unless you get everything back to 100% normal, the environment would have been better off without you. I'm not saying that all efforts
B: Short term, there could be longer environmental damage created. To figure this out, you now have to determine that animal's place in the environment. Assume, for example, that the Zarf Beetle had a cooperating relationship with the Justinian Walrus, residing on the animal's back and eating Avignon fleas that otherwise prey on the Walrus. In the period where the Zarf Beetle populations declined, the Justinian walrus would also lose its population, and Avignon fleas would increase. This chain would get bigger and bigger as the number of parts in the web were further examined (maybe the Justinian walrus was a key food source for the xeno pirnahas, or the Avignon fleas had interactions with Primo trees, all of which would be disrupted). Now, fixing the environment is no longer an issue of just regenerating one species. You'll have thrown an entire ecosystem out of whack.
Humanity claiming the credit for repopulating something it already killed is akin to giving congratulations to a thief who later returned the goods he stole. Nice effort, but you still did some harm. Most animals we save wouldn't be endangered if it wasn't for humans in the first place.
2: Then there's the problem of overcompensation. To many conservationists, it's hard to prove exactly when a species has successfully been repopulated. For example, take whaling. Japan has argued for years that some species of whales have been successfully repopulated as a result of decades of banned whaling. The baleen whale story I posted above is a perfect example of the result: nature creates perfect balances of animal species. Human intervention operates outside this balancing mechanism. Thus, when a population is increased to levels above and beyond what it once was, that species will be forced to migrate to other ecosystems. The link above proves the result: 5 whales were able to take a 100,000 otter population down to 6,000 otters in 5 years.
While the otter may not be considered a keystone species within its environment (yet), we may not know its full role in the environment. Furthermore, it doesn't mean future examples wouldn't involve key species.
3: Even if you do find an instance where humanity is protecting a species of animal or plant that would otherwise be wiped out by nature, it creates a problem. Nature chooses winners and losers in an ecosystem based on that animal's ability to be part of said ecosystem. As a result, the extinction of animals rarely results in the collapse of an ecosystem, because new animals will fill in niches. Thus, human protection of animals that would otherwise go extinct due to nature is the evolutionary equivalent of corporate welfare, allowing species to exist which (Side note: Does this mean God's a capitalist?
).
Arguments 3 and 4 are answered similarly to #1. The ability to intelligently think and to increase supplies of resources can only be considered useful if it serves external purposes. In fact, my indictments of human technology are a reason why the growth of intelligence may be a bad thing.
Now to defend my own arguments.
1) Universal impacts
A) Nanotechnology
In regards to the math behind nanobots being able to overtake the Earth, a few things:
1: Just throwing out an equation isn't enough to prove the argument wrong. You have th justify why each part of your math exists in the whole.
2: We may be overcomplicating this from a mathematical perspective. Quite simply, the only thing that can be proven from this part of the debate is how long it would take for a gray goo outbreak to overwhelm the Earth. The only way winning this argument helps you, then, is that humans get critical time to answer the outbreak. That being said, I'll avoid the math (unless you do something really crazy with it and claim, purely through your calculation, that gray goo won't overwhelm the planet for years after outbreak).
Now to the non-math portion of this debate.
Atomic temperature/composition: Yes, I'll agree that temperature+atomic compounds may interfere with the spread of an outbreak. That being said:
1: An effective gray goo outbreak wouldn't need to use every type of atom on the planet. Remember, nanotechnology doesn't currently claim it can disassemble atoms into their basic parts, then recombine them to form other atoms. More than likely, a gray goo outbreak would involve machines only using the most common atoms, like oxygen, carbon, or hydrogen, simply leaving the other atoms intact (this would also address your equation above: your math assumes that an outbreak would need to consume 100% of matter on the planet). Someone who decided to create a gray goo strain that only built copies of itself with gold, einsteinium, and uranium would pretty much be the most idiotic mad scientist on the planet.
2: In terms of temperature, that's a huge issue which we're not sure about. Generally, however, in excited temperature states, atoms are more easily manipulated. This may be a leap, but considering that a gray goo outbreak would involve a huge amount of chemical and mechanical reactions at once, a good amount of thermal energy would probably be released with the process, bringing atoms to such an excited state. Now, we can't know this for sure... we can't even know the temperatures which could allow gray goo outbreaks anyway... much of this debate is speculative.
As for the production-level barriers:
1: Remember what we're talking about: a single self-replicating nanobot unconstrained. Let's take a look at the odds of this happening:
First, you have, in such a world, billions of various self-replicating machines in hundreds of industries, ranging from agriculture to warfare to simple cleaning tasks. If any one of these gets messed up, you have a problem.
Second, how many humans are around? I'll pretend we're in a theoretical world of 0 population growth between now and then. That means there are 6 billion people in the world. All that would be needed is for one of these people to know enough about nanomachines, and to have the desire, to hack into a single machine and rearange its programming.
Third, there's the glitch possibility. Now, we can't be sure how nanomachines will get their instructions, whether it be through electric pulses, chemical stimuli, or other mechanisms. That being said, we can assume there are some triggering mechanisms to allow humans some control over said machines. With that, all that needs to be done is a simple error with a single molecule, and the whole problem goes to hell in a handbasket.
Fourth, remember that individuals could become the creators. Just as someone could deliberately decide to hack into a nanobot to release gray goo, an individual with enough expertise may be able to create their own self-replicating nanobot, avoiding any possible production barriers.
B) Quantum mining vacuum.
As I said above, no answer. This is 100% cold conceded. No matter how much you may disagree with this scenario, within the context of this debate, you should assume that the argument here is 100% true.
C) Artificial intelligence
Um... why? Why is AI unable to exist? Because it hasn't been created so far? What makes human-level intelligence so unique that it can't be duplicated by a computer? The basis of your argument rests solely on the fact that such a technology hasn't been created yet. That's true of all inventions.
Plus, isn't a human simply a biological machine?
2) Environmental impacts
A) Agriculture
First of all, note the lack of an answer to the Amazon Rain Forest. Even if Flint wins every other part of this debate, losing this scenario means he should automatically lose the debate:
1) The Amazon is one of the richest centers of biodiversity on the planet. You lose that forest, you lose more species just in that region than what was ever saved by humanity.
2) The Amazon provides a huge amount of oxygen for the world.
In addition, the very argument of land use was unanswered. Crops are inherently an invasive species. In order to create a farm, some land inevitably has to be pushed aside, requiring the removal of noneconomic natural resources in order to establish economic resources. The very definition means that biospheres will be destroyed.
B) Biotechnology
Also unanswered. Biotechnology-based plants risk becoming global weeds, wiping out all other plants. This is probably one of the most likely scenarios for destruction of biodiversity. These crops already exist, so it's only a question of a seed escaping containment.
C) Resource extraction
I'll concede this argument, for the most part. However, I want to continue with one argument which I don't see a response to: industrial-level fishing.
D) Monocropping
I'll concede that modern technology prevents erosion from monocropping. That being said, the technologies to sustain said growth create whole new problems. A perfect example of this is fertilizers. Fertilizers in US agriculture have been well documented to seep into the Mississippi River, collecting within the Gulf of Mexico. Once inside the Gulf, the fertilizers remove oxygen from the water, creating large "dead zones" where fish can't live, and fish eggs in the region will overwhelmingly only hatch male fish.
E) Energy output
I'll agree that nature releases more pollutants than human energy output. Don't care about the energy debate anymore. I've got enough ammunition in the other sides of the debate.
F) Species loss
A good portion of my responses to your opening statements are applicable to this debate. That being said, let's look at your arguments.
1) You said primitive man wouldn't care about many species. That's true. However, a couple arguments:
i) First, many of these species didn't conflict with primitive man's needs. The honeybee, for example, doesn't significantly conflict with humans. Yes, an individual bee's nest may threaten nearby humans. However, at best, that means there are isolated incidents of conflict.
ii) Second, large-scale animal removal efforts can't exist in ancient societies. Even if you assume the most drastic scenario that a civilization decided to outright eradicate an animal species, the reach of such a civilization doesn't extend very far. In contrast, modern societies can kill animals at pretty much any location on the planet.
iii) Population levels change the strain of humans on species. In modern society, fishing is needed to feed millions of people throughout the world. The increasing population increases the demand upon nature to provide said resources. In contrast, stone age societies would only have an extremely small fraction, maybe numbering in the couple hundreds at most, pulling resources from any single region of the planet.
2) In regards to the honeybees, you mentioned Chinese and American demand for bees. Your statement utterly ignores the diagnosed issue of Colony Collapse Disorder, which I mentioned previously... http://en.wikipedia.org/wiki/Colony_collapse_disorder
"Colony Collapse Disorder (CCD) or sometimes honey bee depopulation syndrome (HBDS)[1] is a phenomenon in which worker bees from a beehive or European honey bee colony abruptly disappear. While such disappearances have occurred throughout the history of apiculture, the term colony collapse disorder was first applied to a drastic rise in the number of disappearances of Western honey bee colonies in North America in late 2006.[2] Colony collapse is economically significant because many agricultural crops worldwide are pollinated by bees. European beekeepers observed similar phenomena in Belgium, France, the Netherlands, Greece, Italy, Portugal, and Spain,[3] and initial reports have also come in from Switzerland and Germany, albeit to a lesser degree[4] while the Northern Ireland Assembly received reports of a decline greater than 50%.[5] Possible cases of CCD have also been reported in Taiwan since April 2007.[6]"
3) Give me examples of species stone age men hunted to extinction.
4) Here's the trick: Even if modern man doesn't hunt animals to extinction, you still have to defend humans that lived up until now, as prior humans were a prerequisite to achieving the level of technology we have today.
Edit: Mixed up the "Avignon flea" with another flea type
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