The two main components of the Universe that we're familiar with are ordinary matter and light. The matter is mostly atoms, and the light mostly microwaves.
The matter is strongly clumped together to make stars and galaxies separated by vast regions of empty space. But the light is distributed with almost perfect uniformity. The cosmic microwave background is the same everywhere with differences only in the fourth decimal place. The microwave temperature ranges from 2.721 to 2.729 Kelvin across the sky; but matter in a star is 26 orders of magnitude more dense than the isolated atoms we find in the space between galaxies.
We'd like to be able to understand the difference in terms of gravity pulling so much more strongly on the matter compared to the microwaves*. Fair enough. Let's go back to a time when the light and the matter were stuck together. Much earlier in the history of the universe, the radiation was much more energetic and the temperature was much hotter. When it was hotter than about 10,000K there could be no atoms, because the heat was enough to free electrons from their atoms, creating a gas of charged particles, called a plasma.
A gas made of atoms is transparent; light goes right through it. But a plasma is like a dense fog that traps light. So in the hot, early universe, the light and the matter were tied together, such that hotter places were also denser. White noise made random waves that we think account for today's tiny differences in the microwave temperature across the sky.
When the universe was 400,000 years old, the electrons and protons became cool enough to settle down into atoms, and from that point, matter and light were free to go their separate ways. Gravity caused the matter to start clumping, while the light streamed in all directions, nearly unaffected by gravity.
This is a story that was known at the end of the last century, when I was studying astrophysics. In 1997, the observations and the calculations became accurate enough to ask the question whether the known force of gravity could account for all the clumping of matter that has occurred, starting when the universe was 400,000 years old. The answer was "no", and cosmologists started looking for some previously unknown form of matter that they called "dark matter". Compared to the electrons, neutrons, and protons of ordinary matter, there would have to be about 5 times more dark matter to account for the observed clumping.
This is an embarrassment, of course. Scientists don't like to make arbitrary assumptions about a substance that is all around us but which streams right through ordinary matter without interacting, and which evades every form of detection we have ever devised.
But this past summer, the situation has gotten worse, precipitating what Joe Silk calls a "crisis in cosmology". The crisis is this:
What happened in 1997 was that two lines of evidence converged to answer a long-standing question in cosmology. The question was, how fast is the expansion of the universe slowing down due to mutual gravitational attraction. The first lines of inquiry came from refinement of the project begun begun by Edwin Hubble in the 1920s. The redshift of various supernovae in distant galaxies (redshift comes from recession) is plotted against the apparent brightness of those supernovae (apparent brightness is dimmed by distance). The second line is to count galaxies further and further away to get a sense of how much space is out there. Our intuition tells us that if you look a distance r, you see a sphere with area 4πr2. The number of galaxies at distance r should be proportional to 4πr2. But in general relativity theory, space can be structured differently from this. A lot of mass would create a strong gravitational pull, so there is actually less space than 4πr2 for very large distance r.
The two lines are tied together by general relativity theory, which relates the structure of space to the matter in it. Both lines agreed: The expansion isn't slowing down; it's speeding up. And there is actually more space than 4πr2 at large distance r. The implication was that the average mass density of the universe is negative. In response, cosmologists invented the concept of dark energy, a hypothetical substance that has negative mass, which is something that no one has ever seen on earth or in space. Dark matter is a different, unknown substance that it has a gravitational pull and and clumps up like ordinary matter and thins out as the universe expands. But dark energy is spread uniformly and has the same density today as it did when the universe was small. You can't dilute it.
This is strange enough, but Silk's crisis is a further paradox. There is a third way to measure the average density of gravitational matter in the universe, and that involves gravitational lensing of radio waves from the 3 degree background. These radio waves are left over from the glow of ordinary matter when it was opaque, less than 400,000 years after the Big Bang. They are almost but not quite uniform, for reasons that physicists like to explain as statistical fluctuations. And these tiny fluctuations are distorted when we look at them because of gravitational lensing from the matter that the radio waves have passed through along the way. How much gravitating matter would it take to cause the lensing? The answer comes out positive, as though there were no dark energy. So this line of evidence says the expansion of the universe should be slowing down, not speeding up. And the galaxy count should increase less rapidly than 4πr2 at large distance r, when the observations show that the count increases more rapidly.
The venerable Joe Silk says this is a "crisis". Is that too strong a word? Maybe not. The whole science of cosmology is based on the conceit that the physics we study in the laboratory (and in particle accelerators) continues to work at the largest distances and the earliest times. The laws of physics were born with the Big Bang and are the same everywhere and for all time. We've already had to invent two strange, new forms of mass-energy that have never been observed in the lab, which calls the conceit into question. If Silk is right, we might have to modify the laws of physics themselves, and then anything goes. Our conceit was unjustified. Physicists would have to say that the laws we know and understand can't explain what we see. We would lose the science of cosmology. Silk calculates the probability at 3.4 standard deviations, or 99.93%, assuming we hold to Einstein's Theory of Gravity, AKA the General Theory of Relativity.
*Microwaves and other forms of light are also subject to gravity, but the force is too small to be important.