What we don’t know

We are really just at the very beginning of our understanding.   The fact is there is limit to what science knows today.   This is not a matter of a problem. It’s a feature.  It’s exciting.   There is a lot of fun discovery ahead, possibly an infinite amount.   There is no reason to dwell on our failure to understand everything immediately.

We cannot advance until we are aware of what we don’t know as well as what we do know.

Biology / Genetics:

  1. We don’t know how many species are on the planet.   The number varies by an order of magnitude between 4 and 40 million or more.
    1. We don’t know how many go extinct each year naturally
    2. We don’t know how many are created naturally or otherwise each year
    3. We don’t know how many are extinct because of man
    4. We don’t know if more or less extinction is good or what is a “good rate” or a bad rate
  2. We have no idea what almost all of the DNA machines made by our genes actually do or what they affect.
    1. About 25,000 genes are encoded in the 3 billion base pairs in the human genome.  Some of these genes make one or more protein machines.  These machines carry out the primary functions of the body.  Only a small fraction do we have a clue what they might be for or what they do.
    2. We don’t understand the substructure of the protein machines.  The machines show common structure but we don’t know how to parse that into functional elements.  Why or how do the machines do what they do?
    3. In some sense we are simply another level removed from the theory of humors we had 100 years ago with lots of theories of how the organs worked with fluids running around the body.  In a similar way we see protein machines but we have no real understanding of the underlying structure of them.  We couldn’t make one.
  3. We have a miniscule understanding of the epigenetic code that is the program for the human body.
    1. 98% of the genetic code is what used to be called junk DNA just 15 years ago.  Now we understand that the genes are protein machine factories and the real programming of the human body, when to make the gene’s go on and off is encoded in the rest of the DNA.  We also discovered that there is a 5th base pair used in this coding and that in some animals a 6th base pair chemical.
    2. We have only figured out a couple maybe less than 1% of the programming of this epigenetic code.  We don’t know all the things it does, might do or how it really interacts with the genes except for a few special cases.
    3. We know that besides the epigenetic code there is other information stored in the cell.  Chromatin which surrounds the genetic material changes shape at different stages of life and the Telomeres at the ends of the genetic code change what genetic programming is exposed to be used during different stages of life.
    4. In addition we have discovered that  besides mitochondria there are numerous other genetic fragments stored elsewhere in the cell.  There appears to be a storage area for NEW DNA that can be used during a cells lifetime and which is replicated into child cells even though it was acquired during the lifetime of the cell, something that was thought impossible before.
    5. There are other fragments of information and chemicals related to DNA that get copied during cell division that may contain valuable information and process.
  4. We cannot see how the genes react to processes in the body or how really they work or why they get triggered on or off
    1. Due to the microscopic and sensative nature of genomic activity it is hard to capture the actual operations of the genetic machinery.  We are getting better at this.  Being able to find a way to observe this activity closer would be a huge leap in our ability to figure out why or how things work like the microscope to basic biology.
  5. We have no idea how the body is actually built from a single cell
    1. We have some progress here in terms of understanding the basic process abstractly.  However, the specifics are still quite unknown.   As the process of division occurs a program somehow encoded into the DNA and chromatin unleashes and unfurls systematically exposing new programming which drives the cells to diversify and to have certain affinities.   Small variations in this coding can cause limbs to be larger or smaller, be in different places or even have radical impacts on the form that is unleashed.  It is remarkable this works at all considering the complexity.
    2. We also don’t have a good understanding how the process of genetic replication and evolution somehow produces an ever evolving and improving genetic code.  The genetic code is under assault all the time by radiation and chemicals but also from viruses and simply the errors of the process of replication.  We know of numerous means of repair the genetic code has but over time how does the genetic code not degrade or become so confused with all the changes that it is able to produce on the whole essentially a perfect pristine human generation after generation.
  6. We have no idea how the brain works.  Where are our memories?  How are they encoded?  Where does our consciousness arise from or the process of thinking.
    1. We have studied the brain in many ways for many decades.  We have examined animal brains in detail but the basic operations of the brain in terms of thought, learning, memory is unknown.  So, we know that if you do this or that it affects this or that, but why we don’t know.  We don’t know the planning region plans or how we are able to do some of the fantastic things we do.  A very basic thing is memory.  We know memories are stored in the brain, somehow but where or how remains a mystery.  We know some parts of the brain are involved in this or that but how we don’t know.  Again, like the 1900 analogy of having a theory of humors for the organs of the body we have a gross idea of the structure of the brain but only theories how it works and many times these theories are contradictory.
    2. Memories are linked in the brain but we don’t know how this is done.
    3. We don’t understand how the brain forms abstractions or how those abstractions are stored and linked to other memories.
    4. We don’t understand the planning process of the brain
    5. We don’t understand the purpose of brain waves or why they are what they are.  We only know some consequences of some brain wave patterns but no real idea why they exist at all or how they work.
    6. We don’t understand how the brain creates plans of actions say to hit a baseball or drive a car or solve a puzzle.
    7. We don’t understand how the brain has a notion of self and time or thinks in linear steps.  When I say don’t know I am talking about the detailed understanding we have of a motor engine for instance where we can tell you the 4 stroke process and the chemical reactions and what and why everything happens.
    8. We don’t understand how a brain constructs feelings from senses or why those feelings would be the same for people.  For instance, that colors and mixes are the same for different individuals, why we call something beautiful or not.
    9. We don’t understand how we are driven sexually for instance or to eat and how those signals get translated into actions or plans.  How behavior is stored from generation to generation.
  7. We have not been able to replicate the process of learning in any machine in any way like a human although we continue to make better algorithms at recognizing patterns.
    1. Our AI is getting better but be sure we are not close to human level intelligence in the sense of general problem solving and learning.  We can program computers to be better at recognizing things and using that recognition to drive what appears to be intelligence but intelligence isn’t all about recognition or even information.
    2. We have not been able to make a computer that understands humor, can recognize humor or can replicate humor.
    3. We have no program that can recognize beauty, art, understands it or can replicate it.
    4. We have no program that can associate memories with experiential data in a way that is tied to the learning process.
    5. We don’t know what parts of the human consciousness experience are needed or even abstractly are needed to build self-aware computers or intelligent computers or why.  We really don’t understand the what is essential to consciousness.
  8. There are 100,000 chemicals used by the body to maintain us and we don’t know what most of them do.   There are twice as many foreign microbes in our body as our cells and we have no idea what they all do or don’t do.
    1. The human body for all the intense work to study it still consists of a large number of unknown things besides the genetic code talked about before.  Some 100,000 chemicals perform numerous functions the vast majority aren’t understood very well.
    2. Inside the cell the ER (Endoplasmic reticulum) undergoes massive change sometimes in a period of days a cell will manufacture thousands of different chemicals.   In the process the ER will consume itself literally breaking itself apart in constituent elements and then reforming into another structure to produce other chemicals.   This process is remarkably efficient yet also seems expensive and it is not known what stiumulates such change or why and what purpose the new chemicals perform.
  9. We don’t know why we sleep
  10. We don’t know how the body maintains itself or how it responds to damage and knows what to do to fix or repair or replace parts of the body.
    • The homeostatic properties of the body are astonishing.  The body senses thousands or more imbalances of this or that and responds by sending the appropriate machinery to restore balance and repair damage.  We have no idea where that coding is, how the sensing is done in many cases let alone how the body figures out the correct response.
    • The cell is able to consume and reuse waste products frequently perfectly.  This would seem to contradict the idea that over time the cell has to filled with radicals and waste products.  It seems the cell is able to renew itself quite amazingly perfectly.   We don’t know why sometimes it does this and other times let’s waste products and degredation to occur.
    • We don’t know why some organs can grow back and some can’t after damage.
    • We don’t understand if the body needs to degrade or if it is a deliberate process of our genetics. We don’t know in most cases why the body decides to kill cells sometimes and other times lets them live or repairs them.  We don’t understand much of what telomeres do.
    • We recently started understanding the moving machines that transport things inside the cell or outside but have no idea most of the time when or why such transport is initiated.
  11. We don’t know how we smell things and some of the other senses some animals have
    1. It has been estimated that 3,000 of our 25,000 genes are producing machines for detecting smells.  We don’t know how these machines work or how smell works.
    2. Humans seem to have discarded the use of the smell machines or they are non-functional or have been re-purposed in humans.  Obviously smell was a critical function in life in order to devote such a large percentage of the genetic code to it.  We don’t really understand how a dog can detect a single molecule out of the air and recognize it sufficiently to find a trail and follow something for miles.
    3. We have tried to understand how some birds can find their way back home and how they are able to follow certain paths.  Our results seem somewhat contradictory or possibly there are many mechanisms.   Birds seem to have the ability to see the magnetic flux of the Earth’s magnetic field.  While this is extremely useful and has been demonstrated to be part of bird eyes so that they essentially see like a color the magnetic strength in an area.
    4. It is thought that some animals possess the ability to hear extremely low frequency vibrations of the earth which alerts some animals to things like earthquakes and helps birds traverse terrain possibly in combination with their magnetic sense.
  12. We don’t understand the energy balance of the cell and how it operates so efficiently.
  13. Much of the cells operation is a mystery still.
  14. We don’t understand animal language or the extent of animal intelligence and consciousness
    1. It is not understood what types of brain cells are used by animals for what purposes and what capabilities animals have with different size brains or different neurons or different types of neurons.  Some birds with tiny brains are as smart as monkey’s it seems and some animals with thousands of Neurons compared to billions in humans show remarkable intelligence and ability to distinguish faces.   Recently an insect with only 3,000 neurons was shown to be able to distinguish with high specificity to produce behaviors reliably.  We have no idea how this is possible or how it is done.
    2. Bigger animals have more complicated brains and we don’t know many things about these animals awareness, feelings, planning ability.  There yet exists a fantastic need by humans to feel superior to other creatures and to downplay their skill or cognizance.
    3. Nobody has been able to build a computer program that can mimic even the least intelligent creature we know about.
    4. We know that animals communicate yet as smart as we are we have been unable to decipher the language they use to communicate.  Years of studying dolphins, dogs and other creatures have left us still blind about what they say to each other.  I’m not saying they are talking philosophy but there is no doubt they are able to communicate.


  1. We don’t know what Dark matter is which is 20% of the universe.
  2. We don’t know what Dark energy is which is 76% of the universe.
  3. We don’t know the size of the universe.
  4. We don’t know if there are multiple universes.
  5. We don’t know if going back in time is possible.
  6. We don’t know what is behind the event horizon of a black hole.
  7. We don’t know how many dimensions there are in the universe
  8. We don’t think the time and space dimensions are real. They must be emergent but we don’t know emergent from what.
  9. We think time is granular at 10^-43 seconds per tick but the fastest we have ever observed something is 10^-15 seconds.  We have no idea what is happening in the 10^28 clicks between the shortest events we’ve ever seen.  We don’t know if time is granular or not.
  10. We think space is granular at 10^-34 meters but we have never been able to probe to anything less than 10^-16 meters meaning that the smallest thing we’ve ever seem is 10^18 larger than the smallest thing which is equal to the scale of a molecule to the size of the sun.  We don’t know if it is granular.
  11. We don’t know how to do physics or math for a completely discrete granular universe that we think is what we really are.
  12. The laws we have for physics are wrong even though the ones we have seem to work pretty well for most stuff they contradict each other at extremes and none of them can be right because they all fail in some domain.
  13. The vacuum is filled with massive energy bubbling constantly and animating the world.  It is the reason things happen fundamentally.  We have no idea why or how and if it is possible to tap into this somehow.
  14. We don’t understand how the universe can be non-local but it is
  15. We don’t know if there are more particles beyond the recently discovered Higgs and the presupposed graviton or if there are particles with 3/2 spin as predicted by current standard model.
  16. We don’t know the maximum temperature we might achieve superconductivity.
  17. We can’t explain the rate of aging of some stars in some parts of the universe.
  18. We don’t know if the 6 or 7 fundamental constants of nature are really related or random and truly independent.
  19. We don’t know what caused inflation in the early history of the universe or if inflation is the right theory
  20. We don’t know how to combine gravity and quantum mechanics.
  21. We don’t know if information is preserved in a black hole or lost.
  22. We don’t know what time is and why it flows one way other than to invoke probability
  23. In some experiments we’ve seen evidence nature can foresee what we humans will do and act differently based on knowing what we will do.  Our physics requires things can happen in our universe more than a million times faster than the speed of light.  Space can expand faster than the speed of light or contract but we don’t know if we can ever use that.
  24. The math for more than 3 or 4 particles is so complicated and difficult that all the computers on earth could not calculate what will happen to them yet nature does it without a flinch.
  25. The decoherence or measurement problem continues to defy common sense and leads to bizarre things like Many Worlds interpretation that raises even more questions how an infinite number of nearly identical universes could possibly exist
  26. We don’t understand how life could exist since the probability of our universe being existent is less than 1 in 10 to rhe 500.   The constants of nature seemed to be tuned so precisely that varying any of them by even a small amount would result in a completely different universe that probably wouldn’t support evolved life of any kind.
  27. We don’t know if there are more forces than the 4 ( of which 3 are really the same) or if Gravity is really a force of bending of space time or something else. We don’t really know why gravity is 10^39 times weaker than electromagnetic force.


Climate Science

  1. We don’t know much about the oceans in spite of having ARGO probes for 15 years measuring the ocean to 3000 feet.  More than half the ocean is still not measured.   We don’t know what cycles of energy exist in this massive space or what affects the weather in the ocean including biological, chemical or from contact with the mantle, the sun or how geography affects all this.
  2. We don’t know what causes the PDO/AMO ENSO cycles.
  3. We don’t know why the ice ages happen entirely and why they  changed from 40,000 to 100,000 year cycles 3 million years ago or why there weren’t ice ages earlier in the Earths history or why they are happening now.
  4. We can’t explain the temperature record very well in general.
  5. We don’t know what has caused the variations in temperature in the last 150 years or even the cause of the MWP or LIA.
  6. The data we have today on the atmosphere, the ocean, the mantle, the sun are all still extremely spotty and short for even the data we do have.
  7. We don’t understand the mantle and its connection with the core and the surface and any periodic behaviors.
  8. We don’t know why the ice ages show 8C variation in temperature since sunlight variation due to orbital variations can explain less than 10% of this.
  9. We don’t understand if the clouds will warm or cool the atmosphere in reaction to CO2 warming but we know the effect could be much larger than the CO2 temperature change.  We don’t have good ways to measure clouds or understand how clouds happen or why different types of clouds form.
  10. We don’t understand how humidity will change with CO2 warming.  Humidity could be 3 or more times greater than the effect of CO2 on temperature either direction.
  11. The ocean has 1000 times the heat capacity of the atmosphere and any small variation in ocean temperature of even 0.01C could cause tens of degrees change in the atmosphere one way or the other.
  12. The sun is a large ball that supplies all the energy we get on the earth.   We have no understanding of the variations or cycles, currents or atmosphere of the sun and we have no ARGO floats in the sun measuring its weather.
  13. We have trouble computing an accurate “temperature of the earth” today using 14 satellites, thousands of thermostats, ARGO floats and weather balloons as well as other means yet we claim to know what the temperature of the earth in the past from a couple boreholes in a dozen places in the world mostly in some cold regions.
  14. We don’t know why the temperature as measured from satellites, weather balloons, ARGO floats all show half the warming the adjusted land temperatures do.
  15. We have no idea how many species there are in the world or how many go extinct every year or how many are created nor how many of these are due to human causes or naturally happen.
  16. The computer models of the earths atmosphere are broken completely.  The instant we tune them to the past they break for the future.   The computer models don’t model the MWP, LIA or ice ages or any record we have.   We don’t know how to fix them or if they are fixable.

These are hardly complete lists.  Of course there are a million things below this around specific things that we don’t know that are a result of our lack of understanding of these basic things.

Possible other areas to consider such lists :


Human behavior