The most effective strategy to achieve deep understanding that endures is to ask questions—lots of them! I don’t mean questions that provide mere information, although they have their place. The best questions begin with “Why” or “How.” These are questions that ask for evidence and causes.

In the final analysis understanding is personal. Don’t stop asking questions until you are fully satisfied that you can marshal reason and evidence to persuade others of your understanding.

What follows is an approximate transcript of the podcast “Answering Questions by Asking Questions:”

Nothing is more powerful in learning than curiosity. Curiosity inevitably generates questions. Pursuing the answers to questions leads to understanding. Understanding is what makes learning deep as well as durable.

Today’s podcast will work on the question we generated in the previous podcast, Why is it pollution when we burn fossilized organisms and release CO2 and yet living organisms which constantly release CO2 are not a problem?

There’s a lot of bluster about the certainty of climate science these days. Thinking through this focus question is one way to find out what we really know for sure and where ambiguity is reality. I’m not really taking sides in the ongoing debate at this point—just asking a probing question.

It is important to really care when we formulate questions. Maybe you’ve avoided thinking about this issue so far, but the size of one’s carbon footprint has become something of a moral litmus test these days. Advocates claim a scientific mandate for change with existential consequences if we don’t prioritize massive reductions in our carbon footprint. To achieve these reductions will require extraordinary lifestyle changes including vegetarianism, riding your bike, or possibly taking public transportation, and emphasizing utility in clothing rather than fashion. Columbia University lists 35 things you can do to reduce your carbon footprint and it includes these items. The EPA has an online carbon footprint calculator if you want to check your footprint. I link to both in the accompanying blog post at deepanddurable.com.

Rhetorician James Crosswhite in his excellent book, The Rhetoric of Reason, made an interesting observation about asking questions that grab us. He talks about claims that make a claim on us. Here’s a brief snippet (pp. 90-91): “People will not learn to hear claims, and thus will not comprehend the relation between claims and reasons for claims, will not understand arguments as arguments, unless they can ask the questions that allow claims to appear as claims.” Crosswhite argues that we must view a claim as questionable. By questionable he does not mean that we are necessarily skeptical; rather, we take the claim seriously enough that it is worthy of asking questions about the claim and through argument bring evidence and logic to bear on it. That’s what we are doing with our focus question.

We’ve previously recognized divergent, convergent, and metacognitive questions. Formulating the focus question was primarily divergent questioning to generate a question about the carbon cycle that is worthy of our cognitive investment in today’s podcast.

Today we’ll be dealing with a combination of convergent questioning and metacognitive questioning. Convergent questioning is aimed at asking questions that will enable us to converge on an answer. Before we can arrive at an answer, we’ll need to invoke evidence and logic using metacognitive questioning primarily. Metacognition involves thinking about our thinking. Here it will show up by the kind of questions we ask. Our questions will deal with the three aspects of the working layer: questions about our assumptions, questions about facts that are relevant to the focus question, and questions about the ideas (that is the concepts) that form the basis for logical engagement with the question. Along the way we may need to ask questions of clarification when our metacognition signals that  we are fuzzy—we don’t really understand.

Let’s start with the assumptions we will need to make. Acknowledging assumptions is necessary for clear thinking. We all make assumptions because our thinking must start somewhere. We make assumptions about things that our outside our expertise which we accept at face value—at least to begin with. Even within our expertise there are things we accept without proof. As a scientist, an example would be to assume the first law of thermodynamics—matter and energy can neither be created nor destroyed but they can be interconverted. This law is solid. It is as close to proven as is possible in science.

Assumptions can be questioned, however. Sometimes others in a conversation may say something on the order of, you seem to be assuming ______ would you acknowledge that? This might be followed by, why do you think that is a legitimate assumption? A relevant example with the focus question on CO2 levels would be the worldview assumption from one group that the earth is billions of years old and that CO2 levels have been balanced for millions of years assuming uniformitarian principles. On this basis most secular scientists also assume they have access to reliable information about the pre-human past of our planet. On the other side is the assumption based on inferences drawn from scripture that the earth is young and that catastrophes, especially the worldwide flood in Noah’s time have substantially altered earth’s ecosystems. Catastrophism denies that the present is the key to the past. Regardless of where you position yourself, I believe you can generate questions about the assumptions that are being made here.

Here's another question: Why is it a legitimate assumption that global scale phenomena can be explained by extrapolation of local ecosystem level causes and effects? That is certainly an assumption that climate scientists make. Here’s one final question about assumptions. Most everyone scientist and layperson alike would answer yes to this question: Is it always desirable that organic compounds be biodegradable? This will prove to be relevant later in our discussion. One limited expression of this is that every naturally occurring organic compound is food for some living organism which will break it down in order  to stay alive. On this basis we can expect that oil spills will eventually be degraded by microorganisms and the ecology of the spill area will return to at least some semblance of its original condition.

We reason primarily within our conceptual frameworks. Many people trip over the use of the label concept. A concept is a perceived pattern, a regularity. By constructing concepts, we simplify multiple occurrences into powerful ideas that are flexible and extensible to a variety of contexts. As a simple example let’s take war. War involves hostility between adversaries that precipitates taking actions to harm the adversary. It may involve armed conflict, but it might be a cyberattack. There are entire war colleges which study the history of wars, the prevention of wars, the justification of wars, and the conduct of wars. There is much to think about, but beneath it all there is the singular concept, the idea of war.

Let’s consider our focus question: Why is it pollution when we burn fossilized organisms and release CO2 and yet living organisms which constantly release CO2 are not a problem?

Two main concepts emerge as we chew on this. Cycling and sequestering. The carbon cycle is the mechanism by which we expect that CO2 will be kept at a constant and acceptable level. Part of the way that the cycle keeps CO2 levels constant is through sequestration. Let’s try to get closer to an answer by asking conceptual questions.

The focus question uses the phrase “release CO2” twice. Here are a few questions that come to mind. What processes release CO2? What processes produce substances from which CO2 can be released?

These questions are necessitated by the concept of a cycle. Cycles repeat over and over. Answering these two questions we come up with the three major types of organisms that are responsible for cycling carbon. Producers capture CO2 and use it to manufacture—that is produce—various organic molecules. Consumers and decomposers both use those organic molecules as fuel and release CO2 as a waste product.

What about sequestration? To sequester is an alternative to the merry-go-round concept of a cycle. It’s an opt out situation. That suggests these questions: How can organic molecules be sequestered? Can CO2 be sequestered? Is sequestration reversible? Is sequestration regulated? How is sequestration related to biodegradability? When we start to answer these questions, we are entering the third aspect of the working layer and that is the realm of facts. I’ll deal later with questions about facts, but grappling with conceptual questions necessitates at least a few basic factual answers that have already been offered. We can question those answers later, and we will.

The total carbon on planet earth is constant as recognized in the first law of thermodynamics. The carbon cycle aims to keep CO2 levels constant. However, when organic molecules are not degraded (broken down by metabolism) to CO2 they are sequestered and the carbon they contain is effectively removed from the carbon cycle. This would lower CO2 levels over time. That’s what happened in the past when living organisms were fossilized to produce fossil fuel deposits deep in the earth. Their organic biomass was effectively removed from the carbon cycle. Sequestration is also what happens when producers create biomass and, in the process, create more cells and more offspring. For as long as they are alive, their organic biomass is maintained and is not converted into CO2. If producers like green plants are eaten by other organisms (which we call consumers) such as humans or animals, plant biomass is converted into human or animal biomass. Upon the death of living organisms of all types, decomposers convert organic biomass into CO2. Thus, the greater the population of living organisms, the greater the amount of sequestered carbon.

This raises another question. Since living organisms continually use organic molecules as fuel to stay alive, doesn’t this constantly release CO2? The answer, of course, is yes and the longer an organism lives, the more CO2 release predominates over the amount of sequestered carbon in their biomass. This means longer living organisms have a bigger carbon footprint.

Within these concepts we can now ask this question: What made the organic biomass of fossilized organisms stable and not susceptible to decomposition into CO2? The answer is that the process of fossilization involving heat and pressure transformed their chemical makeup into much more stable organic compounds through a process called diagenesis. These same conditions also may have sterilized the immediate environment where the fossils were formed so that decomposition couldn’t touch them.

I’ll conclude by considering a few facts which are pertinent to the focus question.

Facts are the result of someone’s previous thinking employing the core, working, and output layers. Because of this personal dimension, I don’t think brute uninterpreted facts exist. Facts need to be respected and viewed as highly probable, but not idolized as absolute. Most facts represent truth, but there may be exceptions where the truth doesn’t apply for various reasons. There is frequently a collision between a scientific hypothesis and stubborn facts. This is sometimes noted by the wry humor of this statement: “The tragedy of science; a beautiful hypothesis slain by an ugly fact.” Even when science and facts appear to agree, reigning scientific paradigms appear to be secure until they aren’t as Thomas Kuhn points out in his book, The Structure of Scientific Revolutions. It starts when new and different questions are asked. These questions suggest new experiments. When experiments are done that produce solid evidence that falsify the current dogma, there is first a period of ad hoc theory patching until there are more patches than theory. This patching period continues until someone advances a hypothesis that explains the experimental results including the so-called anomalies. Once an alternative hypothesis gains adherents the old dogma falls hard and fast.

I confess that in preparing this podcast I spent a fascinating 45 minutes sparring with ChatGPT over some inconvenient facts related to the focus question on CO2 emissions. If you want to see our full “conversation” you can go to the blog post that accompanies this podcast episode. You’ll find it at deepanddurable.com

ChatGPT regularly offered up as unassailable fact the same truisms that you read in the popular news media or hear on television. When challenged with facts that didn’t support the popular narrative, ChatGPT slowed down substantially and its output—initially almost instantaneous—appeared word by word on the screen. At one juncture as ChatGPT was backing itself into a corner and edging toward contradiction of what it had said earlier, the response on screen turned red and froze uncompleted. To get the response going again I had to click on a button that would regenerate the conversation. It then proceeded to take a different, more generic tack in answering my query. Unfortunately, the red screen response disappeared and isn’t part of the file you’ll see in my blog post. The ChatGPT “discussion” covered more details than we’ll have time for in this podcast but its failure to fully answer questions as well as its factual errors is instructive.

Let’s examine a few established facts that are inconvenient for the standard narrative regarding the sources of rising CO2 levels in the atmosphere. In the standard narrative CO2 is “emitted” by humans and animals but captured by green plants as part of photosynthesis. The truth is that nearly all life forms release CO2. The main exceptions are bacteria and other prokaryotic life forms that ferment organic molecules. Fermentation occurs when the waste products of metabolism are themselves organic. The production of lactic acid and other organic acids in cheese making is one example of fermentation. The alcoholic fermentation itself produces both ethyl alcohol (which is organic) and CO2 which is responsible for the bubbles in the brew.

Reality is much more complicated than plants are the good guys and animals are the bad guys. It is necessary to ask the appropriate questions that unearth the truth. I wish we had the time to articulate what follows in the form of questions, but I’m getting close to my time limit for this podcast. You can see some of my questions in the ChatGPT document at my blog. You can also infer the questions I’m asking  from the facts I marshal, ala Jeopardy.

Plants take up CO2 from the atmosphere and they use this source of carbon along with light energy to produce all the organic molecules that make up plant cells. Some of these organic molecules are used as fuel. Fuel molecules are dismantled to release their energy in the mitochondria found in the same plant cells. The waste products from this breakdown are water and CO2. CO2 is preferentially captured by the chloroplasts of the same cell.   

During daylight with adequate moisture and favorable temperatures photosynthesis captures enough CO2 to cause cell growth and, eventually cell division which causes the plant itself to grow. Only a fraction of the CO2 captured ends up as fuel. Most of it ends up as biomass that enables growth when conditions are favorable. Most of the CO2 is used to make the DNA, protein, carbohydrates, and lipids out of which bigger cells and more cells will be constructed.

It's a different story when conditions are not favorable for photosynthesis. This is true when it’s dark and photosynthesis is impossible. It is also true when other conditions are unfavorable for growth. Under these conditions cellular respiration breaks down organic food molecules and CO2 is released into the air, just as in animal cells.

Plants are not the only players in the CO2 capture game. Bacteria engage in several distinct types of photosynthesis. In addition, a group of microbes called Archaea capture CO2, but use inorganic chemical energy, rather than light energy to make their own organic molecules.

When I asked ChatGPT about the contribution of bacteria to CO2 uptake, things got really slow and the AI engine mischaracterized their contribution. Prokaryotic cells including bacteria and Archaea are indeed  very small, but their collective biomass is at least as great as all the plants and animals on earth combined. The marine cyanobacterium Prochlorococcus marinus is “arguably the most abundant photosynthetic organism on our planet.” It was first discovered in 1986. (Microbe 2e, Swanson et al. ASM Press, p. 402.) Prokaryote metabolism is significantly more efficient than plants and animals (contra ChatGPT) enabling them to grow and multiply much more rapidly than plants or animals. Their contribution to the global cycling of carbon is left out because they are extraordinarily diverse and mostly undiscovered or uncharacterized. Out of an estimated 10 million species of prokaryotes, only perhaps 10,000 or so have been studied in any detail.

This microbial ignorance has gotten ecologists in trouble in the past. I asked ChatGPT about the problems uncovered in a project called Biosphere 2 that launched in the 1990’s. Biosphere 2 was created as a very large (3.14 acre), sealed environment with seven interacting biomes inhabited by plants, animals, and eight humans. Biosphere 2 was meant to be fully self-sustaining as if it were isolated from the earth. They termed the earth itself Biosphere 1. In the first mission Biosphere 2 oxygen levels dropped dangerously over 16 months to levels like living at about 13,400 ft. Microbes in the rich soil apparently consumed far more oxygen than anticipated.

Here’s one account of the first Biosphere 2 mission:

“Managing CO2 levels was a particular challenge, and a source of controversy regarding the Biosphere 2 project's alleged misrepresentation to the public. Daily fluctuation of carbon dioxide dynamics was typically 600 ppm because of the strong drawdown during sunlight hours by plant photosynthesis, followed by a similar rise during the nighttime when system respiration dominated. As expected, there was also a strong seasonal signature to CO2 levels, with wintertime levels as high as 4,000–4,500 ppm and summertime levels near 1,000 ppm.”

CO2 levels in the earth’s atmosphere on the other hand were 420 ppm in February, 2023 up from about 317 ppm in 1960. Efforts in Biosphere 2 to rebalance the ecosystems were unsuccessful and scientists had to bootleg in oxygen and artificially scrub CO2 to keep from endangering its human inhabitants. Indeed, most of the vertebrate animals in Biosphere 2 perished in the initial experiments from 1991-1993. One more attempt at operating Biosphere 2 as a closed system in 1994 also failed to achieve its objectives. Biosphere 2 is no longer operated as a closed system but it  is still used to investigate large scale model biomes. Scientific American titled a 2021 article “Biosphere 2: The Once Infamous Live-in Terrarium is Transforming Climate Research.”

Here are links to two YouTube videos on Biosphere 2.

Romanticized view prior to first mission: https://www.youtube.com/watch?v=GWKghqOajDo&t=202s

Promotional for open system version as currently operated by the University of Arizona: https://www.youtube.com/watch?v=egolqUikA8c

If we can’t manage an artificial highly controlled environment in Biosphere 2, and the global earth operates on the same principles, it follows that we can’t manage global phenomena. Whether we need to be involved in management and what actions might be most salutary is the topic for the final episode of this season’s podcasts. Join me in two weeks as we move our focus question into the output layer of thinking and develop an answer as well as determine appropriate actions.

I think you will find my “discussion” with ChatGPT illuminating in a variety of ways. I’ve posted my interaction below.

Via ChatGPT on 3/15/23 (Bold, italicized questions and statements are mine; the rest was generated by ChatGPT)

Why is it pollution when we burn fossilized organisms and release CO2 and yet living organisms which constantly release CO2 are not a problem?

While it is true that living organisms release carbon dioxide (CO2) through respiration, the difference between this and burning fossil fuels is the rate and scale of the release.

Fossil fuels, such as coal, oil, and gas, are the remains of prehistoric plants and animals that have been buried for millions of years. When we extract and burn these fuels, we release carbon that was trapped underground for a very long time, and this sudden release of carbon dioxide is causing a rapid increase in the concentration of greenhouse gases in the atmosphere.

On the other hand, living organisms release CO2 as part of the natural carbon cycle, which has been in balance for millions of years. Plants absorb carbon dioxide through photosynthesis, while animals and other organisms release it through respiration. This cycle maintains a relatively stable concentration of carbon dioxide in the atmosphere.

However, human activities, such as burning fossil fuels and deforestation, are causing an imbalance in the carbon cycle by releasing more carbon dioxide into the atmosphere than can be absorbed by natural processes. This leads to a buildup of greenhouse gases, which trap heat in the Earth's atmosphere and cause global warming, climate change, and a host of negative environmental impacts.

Therefore, while it is true that living organisms do release carbon dioxide, the difference lies in the scale and rate of release, and the fact that human activities are upsetting the natural balance of the carbon cycle.

Weren't CO2 levels much higher in the distant past than they are now? Why was this higher level not a problem then, but it is now?

It is true that carbon dioxide (CO2) levels in the Earth's atmosphere have been much higher in the distant past than they are today. However, the climate and environmental conditions of those times were also very different from what we have today.

During the geological past, there have been periods of high CO2 concentrations, such as the Carboniferous Period, which occurred over 300 million years ago, when atmospheric CO2 levels were up to 10 times higher than they are today. However, the Earth's climate was also very different during these times. For example, during the Carboniferous Period, the Earth was much warmer, with a tropical climate that supported the growth of vast forests that eventually became coal deposits. Additionally, there were no ice caps at the poles, and sea levels were much higher than they are today.

In contrast, today's global climate is much different from the conditions that existed during these periods. Human activities, such as the burning of fossil fuels, deforestation, and industrial processes, are leading to an increase in atmospheric CO2 levels at an unprecedented rate. This is causing a rapid and dramatic shift in the Earth's climate, with more frequent and severe heat waves, droughts, wildfires, floods, and other extreme weather events. Additionally, the increase in CO2 levels is causing ocean acidification, which is threatening the survival of many marine species.

In summary, while there have been periods of high CO2 concentrations in the past, the difference today is the speed and scale of the increase in CO2 levels, which is leading to unprecedented and rapid changes in the Earth's climate and ecosystems.

How do you know the rate of change in CO2 is unprecedented?

Scientists can estimate past levels of atmospheric CO2 using a variety of methods, such as analyzing air bubbles trapped in ice cores, studying the chemical composition of ancient sediments and rocks, and measuring the carbon content of plant and animal fossils. These methods have allowed researchers to reconstruct a record of atmospheric CO2 levels going back hundreds of thousands or even millions of years.

Based on this record, scientists have determined that the current rate of increase in atmospheric CO2 levels is indeed unprecedented. For example, according to the US National Oceanic and Atmospheric Administration (NOAA), the current atmospheric CO2 concentration is around 420 parts per million (ppm), which is higher than at any time in at least the last 800,000 years. Additionally, the current rate of increase in CO2 concentration is around 2-3 ppm per year, which is much faster than any natural increase in CO2 levels that has occurred over the last several hundred thousand years.

Furthermore, the rate of CO2 increase is much faster than the natural carbon cycle can absorb or mitigate it. The natural carbon cycle is a complex process that involves the exchange of carbon between the atmosphere, land, and oceans. The cycle usually operates on a geological timescale, taking tens of thousands or even millions of years for CO2 to be absorbed or released. In contrast, human activities such as burning of fossil fuels and deforestation are releasing CO2 at a rate that is much faster than the natural carbon cycle can handle.

Therefore, based on this evidence, we can conclude that the current rate of increase in atmospheric CO2 levels is unprecedented in the geological history of the Earth.

Don't cycles have the ability to balance themselves?

Yes, natural cycles in the Earth's system, including the carbon cycle, have the ability to balance themselves over long periods of time. However, the rate and scale of human activities are currently upsetting the balance of the carbon cycle and other natural cycles, leading to unprecedented changes in the Earth's climate and ecosystems.

The carbon cycle is a natural process that involves the exchange of carbon between the atmosphere, oceans, land, and living organisms. This cycle has been in balance for millions of years, with the rate of carbon uptake and release generally equal. However, human activities, such as the burning of fossil fuels and deforestation, are releasing more carbon into the atmosphere than the natural carbon cycle can absorb, leading to a buildup of greenhouse gases that trap heat in the Earth's atmosphere and cause global warming and climate change.

While natural processes in the carbon cycle, such as the uptake of carbon by oceans and vegetation, can help mitigate the effects of increased carbon emissions, these processes take time and are limited in their ability to absorb the large amounts of carbon being released by human activities. Additionally, other cycles, such as the nitrogen cycle and water cycle, are also being impacted by human activities, leading to further ecological disruption.

Therefore, while natural cycles do have the ability to balance themselves over long periods of time, the rate and scale of human activities are currently disrupting the natural balance and leading to unprecedented changes in the Earth's climate and ecosystems.

Your earlier response indicated simplistically that plants absorb CO2 while animals produce it. Plants also produce CO2 through respiration. Respiration in plants breaks down organic fuel molecules produced by photosynthesis. It stands to reason that the CO2 produced through respiration in plant mitochondria would make a substantial contribution to the CO2 fixed in photosynthesis within chloroplasts in that same plant cell.

You are correct that plants also produce CO2 through respiration, which is the process by which organic fuel molecules produced by photosynthesis are broken down to release energy. This process occurs in all living cells, including plant cells. During respiration, glucose and oxygen are consumed, and carbon dioxide, water, and energy are produced.

The CO2 produced during respiration in plant cells is generally balanced by the CO2 absorbed during photosynthesis, and the net effect of photosynthesis is to remove CO2 from the atmosphere. However, the rate of CO2 uptake by photosynthesis and the rate of CO2 release by respiration can vary depending on environmental factors such as temperature, light availability, and water availability.

In general, during the day when there is sufficient light, the rate of photosynthesis is higher than the rate of respiration, and plants absorb more CO2 than they release. However, at night or under low light conditions, the rate of respiration can exceed the rate of photosynthesis, and plants release more CO2 than they absorb.

Overall, the contribution of plant respiration to the global carbon cycle is relatively small compared to the emissions from human activities such as burning fossil fuels. However, it is important to understand the role of respiration in plant carbon cycling and how it interacts with photosynthesis to influence the net uptake or release of CO2 by plants.

You haven't addressed the fate of CO2 released by mitochondria in plant cells. Isn't it fixed in the chloroplasts of the same cell?

I apologize for the confusion in my previous response. You are correct that the CO2 produced by respiration in plant cells is not necessarily released into the atmosphere but rather can be used in the same cell during photosynthesis.

During photosynthesis, the chloroplasts within plant cells use energy from sunlight to convert CO2 and water into glucose and oxygen. This process takes place in the thylakoid membranes and stroma of chloroplasts. The CO2 required for photosynthesis can come from the atmosphere or from the CO2 produced by respiration within the plant cell.

Therefore, the CO2 produced by respiration in plant mitochondria can be used in the same cell during photosynthesis to produce glucose and oxygen. This process results in a net uptake of CO2 from the atmosphere, as the carbon fixed in glucose molecules during photosynthesis is stored in the plant's biomass.

It's worth noting, however, that not all of the CO2 produced by respiration is necessarily used in photosynthesis within the same cell. Some of the CO2 may diffuse out of the cell and into the surrounding environment or be transported to other parts of the plant for use in photosynthesis. The fate of the CO2 produced by respiration depends on various factors such as the rate of respiration and photosynthesis, environmental conditions, and the physiology of the plant.

I believe photosynthesis generates glyceradehyde -3-phosphate, not glucose. Plants can make all of their organic molecules from glyceradehyde -3-phosphate. They generally store excess food molecules as sucrose or starch, not as glucose. As far as releasing oxygen, plants produce oxygen via photosynthesis within chloroplasts, but they consume oxygen in the mitochondria. Respiration in the mitochondria uses O2 as the terminal electron acceptor and water is produced as a result. It seems, therefore that the quantity of O2 that plants release into the environment is significantly diminished, if not altogether eliminated by this reality.

You are correct that photosynthesis generates glyceraldehyde-3-phosphate, not glucose, as an initial product. Glyceraldehyde-3-phosphate can then be used to synthesize a variety of organic molecules, including glucose, fructose, and sucrose, depending on the needs of the plant.

Regarding the production of oxygen, you are also correct that plants release oxygen into the atmosphere during photosynthesis, but they consume oxygen during respiration. However, the oxygen produced during photosynthesis is in excess of the oxygen consumed during respiration, so the net effect is a release of oxygen into the atmosphere. The amount of oxygen produced during photosynthesis is typically several times greater than the amount consumed during respiration, so plants are net producers of oxygen.

It's also worth noting that the rate of photosynthesis and respiration in plants can vary depending on environmental conditions such as light, temperature, and humidity. Under certain conditions, such as prolonged darkness or high temperatures, the rate of respiration can exceed the rate of photosynthesis, leading to a net consumption of oxygen and release of carbon dioxide by the plant. However, under normal conditions, plants are net producers of oxygen and net absorbers of carbon dioxide.

What is the biochemical basis for your statement that the oxygen produced during photosynthesis is in excess of the oxygen consumed during respiration?

The biochemical basis for the statement that oxygen produced during photosynthesis is in excess of the oxygen consumed during respiration comes from the stoichiometry of the chemical reactions involved in photosynthesis and respiration.

During photosynthesis, the overall reaction is:

6 CO2 + 6 H2O + energy (light) → C6H12O6 (glucose) + 6 O2

This reaction shows that for every molecule of glucose produced, six molecules of carbon dioxide and six molecules of water are consumed, and six molecules of oxygen are produced.

During respiration, the overall reaction is:

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy (ATP)

This reaction shows that for every molecule of glucose consumed, six molecules of oxygen are consumed, and six molecules of carbon dioxide and six molecules of water are produced.

The net effect of photosynthesis and respiration is to produce glucose and oxygen from carbon dioxide and water. The glucose can be used by the plant for energy or to synthesize other organic molecules, and the oxygen is released into the atmosphere. During respiration, the plant consumes the glucose and oxygen to produce carbon dioxide, water, and energy. However, the amount of oxygen produced during photosynthesis is typically several times greater than the amount consumed during respiration, resulting in a net release of oxygen into the atmosphere.

In other words, the net effect of photosynthesis and respiration is a transfer of energy from sunlight to chemical energy in the form of glucose and a release of oxygen into the atmosphere.

Your stoichiometry shows 6 O2 produced in photosynthesis per glucose molecule generated and 6 O2 used per glucose molecule consumed in respiration. This looks like balance and not net production of oxygen, much less a support for your statement "the amount of oxygen produced during photosynthesis is typically several times greater than the amount consumed during respiration." Where would this extra oxygen come from?

I apologize for the confusion in my previous response. You are correct that the stoichiometry of photosynthesis and respiration shows a balance of oxygen, with six molecules of oxygen produced during photosynthesis for every six molecules of oxygen consumed during respiration. The net effect of photosynthesis and respiration in terms of oxygen production and consumption is dependent on the rate of each process.

During the day, when light is available for photosynthesis, the rate of photosynthesis is typically greater than the rate of respiration in plants, resulting in a net production of oxygen. The excess oxygen produced during photosynthesis is released into the atmosphere. During the night, when there is no light for photosynthesis, the rate of respiration typically exceeds the rate of photosynthesis, resulting in a net consumption of oxygen and production of carbon dioxide by the plant.

Overall, the balance of oxygen during photosynthesis and respiration means that the net effect of plant metabolism on atmospheric oxygen levels is dependent on the rate of photosynthesis relative to the rate of respiration. When the rate of photosynthesis is greater than the rate of respiration, oxygen is produced and released into the atmosphere. When the rate of respiration is greater than the rate of photosynthesis, oxygen is consumed and carbon dioxide is released into the atmosphere.

Prokaryotic organisms also engage in various forms of autotrophic metabolism by which CO2 is fixed including photosynthesis. The biomass of such prokaryotes is believed to exceed that of green plants. Prokaryotes are also significantly more adaptable than green plants. It seems that prokaryotes could have a significant near term influence on lowering atmospheric CO2.

You are correct that prokaryotic organisms, including various types of bacteria, engage in autotrophic metabolism, including photosynthesis, by which they fix CO2 into organic compounds. Prokaryotes are known to play important roles in biogeochemical cycling, including carbon cycling, and are estimated to contribute significantly to global primary production.

However, while prokaryotes may have a role to play in regulating atmospheric CO2 levels, there are several factors that limit their potential to significantly reduce atmospheric CO2 in the near term.

Firstly, the rate of carbon fixation by prokaryotes, including through photosynthesis, is generally lower than that of green plants. While prokaryotes may be more adaptable than green plants, they are also generally smaller and have lower energy requirements, which limits their capacity for carbon fixation.

Secondly, prokaryotes are subject to similar environmental stresses as green plants, including changes in temperature, pH, and nutrient availability, which can limit their growth and carbon fixation capacity.

Finally, even if prokaryotes were able to significantly reduce atmospheric CO2 levels in the short term, the effects may be temporary, as changes in atmospheric CO2 levels can affect global climate and alter environmental conditions, potentially favoring other types of organisms that may then contribute to increased atmospheric CO2 levels.

Overall, while prokaryotes are important players in biogeochemical cycling, it is likely that a combination of different organisms and processes, including green plants and various types of bacteria, will be necessary to effectively mitigate and regulate atmospheric CO2 levels in the long term.

A misjudging of the importance of bacteria in the rich soil of Biosphere 2 was responsible for the need for supplemental oxygen as well as CO2 scrubbing. This showed an inability to regulate and balance the various interacting ecosystems in Biosphere 2. Has Biosphere 2 since been able to achieve internal balance including in the carbon cycle without resorting to artificial interventions?

Biosphere 2 was an experimental facility designed to explore the potential for creating self-sustaining ecosystems in a closed environment. It included several different ecosystems, including a rainforest, an ocean, a savanna, and a desert, as well as human living quarters.

During the initial two-year mission of Biosphere 2 in the early 1990s, the facility experienced several challenges, including issues with oxygen and CO2 levels, as well as challenges with the soil microbiome, which affected the growth of crops and other organisms. These challenges were partly due to the complex and interconnected nature of the ecosystems within the facility, as well as a lack of understanding of how to effectively manage and regulate the internal environment.

Since then, the management of Biosphere 2 has been taken over by the University of Arizona, and the facility has undergone extensive renovations and improvements. Today, Biosphere 2 is used primarily as a research facility, and research conducted at the facility has yielded insights into a variety of topics, including global climate change, biogeochemical cycling, and ecosystem dynamics.

While Biosphere 2 has made significant strides in improving its management and understanding of its internal ecosystems, it is not entirely self-sustaining and still requires some external inputs, such as water and energy, to maintain its operations. Additionally, the facility is still used primarily for research and experimentation rather than as a self-sustaining ecosystem for human habitation.

Doesn't the inability to balance the ecosystems in Biosphere 2 without human intervention demonstrate a lack of understanding of biogeochemical cycling? Doesn't that reality also raise questions about how complete our understanding of global biogeochemical cycling is?

The challenges encountered in Biosphere 2 during its early missions did indeed demonstrate that there are still many unknowns and complexities associated with biogeochemical cycling in closed ecosystems. The inability to balance the various ecosystems within Biosphere 2 without human intervention suggests that there is still much to learn about the dynamics of these systems and the factors that influence their stability and resilience.

At the same time, it's important to recognize that Biosphere 2 was a highly controlled and experimental environment, and the challenges encountered there may not necessarily be representative of the complexities of biogeochemical cycling in natural ecosystems. While the facility provided valuable insights into the dynamics of closed ecosystems and the challenges of creating self-sustaining environments, it's important to continue studying these processes in a variety of different settings and under different conditions to build a more complete understanding of biogeochemical cycling on a global scale.

Overall, our understanding of biogeochemical cycling is constantly evolving as new research is conducted and new technologies and methodologies are developed. While there is still much to learn, scientists and researchers continue to make progress in this field, and this knowledge is critical for developing effective strategies for mitigating the impacts of global environmental changes.

This appears to be a clear case of an argument from the lesser to the greater. If balance can't be achieved in the "highly controlled and experimental environment" of Biosphere 2, then we certainly wouldn't expect to understand "biogeochemical cycling on a global scale" sufficiently to be speaking with authority about what causes elevated CO2 in the atmosphere and how it can best be remediated.

While it is true that the complexity of biogeochemical cycling increases with scale, it is important to note that the principles and mechanisms that govern these processes at a small scale are still applicable at a larger scale. Our understanding of biogeochemical cycling is based on a combination of empirical observations, theoretical models, and experiments at various scales.

While it is true that the challenges encountered in Biosphere 2 demonstrate that there are still uncertainties and complexities associated with closed ecosystem dynamics, this does not necessarily mean that we cannot speak with authority about global biogeochemical cycling or the causes of elevated CO2 in the atmosphere. Scientists have made significant progress in understanding the biogeochemical cycling of carbon and other elements on a global scale through a combination of observations, models, and experiments. This knowledge has led to a better understanding of the factors that contribute to elevated CO2 in the atmosphere, including the burning of fossil fuels and changes in land use, and has informed efforts to mitigate these impacts through strategies like carbon capture and storage and afforestation.

While our understanding of biogeochemical cycling is constantly evolving, and there is still much to learn, the scientific community has made significant progress in this field, and this knowledge is critical for developing effective strategies to address global environmental challenges.

What made the organic biomass of fossilized organisms stable and not susceptible to decomposition into CO2?

The organic biomass of fossilized organisms became stable over millions of years because it was buried in sedimentary rock layers and subjected to high pressure and temperature. This process, known as diagenesis, causes the organic matter to undergo chemical changes that transform it into more stable compounds, such as hydrocarbons, coal, and petroleum.

During diagenesis, the organic matter is subjected to high temperatures and pressures, which cause it to lose water and other volatile components, as well as undergo chemical reactions that break down complex organic molecules into simpler compounds. This process results in the formation of fossil fuels, which are primarily composed of hydrocarbons such as methane, oil, and coal.

The stable nature of fossilized organic biomass is due to the fact that it has undergone these chemical changes, which have made it resistant to further decomposition. However, when we burn these fossil fuels, we release the carbon that was stored in them back into the atmosphere in the form of CO2, where it can contribute to climate change.