Why is the universe like a tortoiseshell cat?

COBE CMB fluctuations. Original Source: NASA

All tortoiseshell cats are female.  Males can be black, or ginger, but never tortoiseshell.  The reason for this is that the mechanism by which tortoiseshell cats get the patterns on their coats depends on having two X chromosomes.  This is all described beautifully in Chapter 7 of "Junk DNA", by Nessa Carey.

Females have twice as many X chromosomes as males, which on the face of it should result in 100% more expression for the genes on that chromosome.  This should lead to much greater differences between males and females than we actually see.  To put this in perspective, Down's syndrome is caused by individuals having 3 copies of chromosome 21 instead of 2.  But this is a far smaller chromosome than X and the difference is only 50%, rather than 100%.  (The fact that chromosome 21 is so small is the reason Down's syndrome is more common than syndromes in which there are too many copies of more important chromosomes.  Having too many of those is more likely to lead to miscarriage.)

The reason we see similar levels of gene expression for the X chromosome in males and females is that in females one copy of the X chromosome is deactivated.  A region of DNA on the X chromosome called the X inactivation centre produces an RNA molecule called Xist (for "X inactive specific transcript").  Actually the X inactivation centre produces two RNA molecules. The other one is called Tsix and is created by reading the other strand of DNA in the opposite direction.  In most cells one X chromosome expresses Xist RNA and the other expresses Tsix RNA.  Xist RNA "paints" the remainder of the chromosome that produces it, causing it to curl up into a useless inactive little ball called a Barr body.  Meanwhile the Tsix producing X chromosome remains unfurled and behaves just like any other chromosome. In males there is only one X chromosome and this remains active and unfurled. This is why cells from males and females express X chromosome DNA to more or less the same extent.

This inactivation pattern is inherited during cell division.  So, for example, if the X chromosome from Dad is deactivated in a given cell, and that cell divides, then the the X chromosome from Dad will also be deactivated in the two daughter cells.  On the other hand if it was the X chromosome from Mum that was deactivated then this will be the case in the daughter cells too.  This means that the ancestry of each cell can be traced back to some cell in which the decision to inactivate either Mum or Dad's X chromosome was made.  It turns out that this happens in all cells, more or less simultaneously, when the embryo reaches about 100 cells in size.  And the decision in each cell is made randomly and independently of the other cells.

Finally we can understand why tortoiseshell cats have the pattern that they do and why all tortoiseshells are female.  The reason is that the gene for ginger fur and the gene for black fur are inherited via the X chromosome.  Tortoiseshells inherit ginger from one parent and black from the other.  When the embryo reaches about 100 cells each cell decides to inactivate either the ginger X chromosome or the black X chromosome.  Some of these 100 cells ultimately become ancestors of fur follicles, resulting in somewhat fewer than 100 patches of ginger and black.

So the pelt of a tortoiseshell cat is an historical snapshot, freezing an event that occurred in the early development of the embryonic kitten.  And my Thought For The Day is:

That's a bit like the Cosmic Microwave Background.

In the first few minutes after the Big Bang our universe was hot enough for nuclear fusion to be possible everywhere (whereas this now only happens in the cores of stars).  During this time about 25% of the hydrogen was converted into helium, resulting in a hot plasma of the two elements in which electrons were not bound to nuclei.  This plasma lasted until around 400,000 years ATBB(*), by which time the expansion of the universe had cooled the plasma enough for atoms to form.  This generated a large amount of electromagnetic radiation, which we see today - at much lower frequencies due to expansion - as the Cosmic Microwave Background.  This is all described much more fully - and more beautifully - in "Our Mathematical Universe", by Max Tegmark.

At first it was believed that the CMB would be the same intensity in all directions. After all, the Big Bang is should be a symmetric event, which should lead to a homogeneous plasma soup 400,000 years later.  Initial measurements seemed to support this, but as the accuracy of these measurements improved an anisotropic pattern emerged in which the intensity varied by around 0.002%.  Plotting these differences you see a "blotchy" pattern emerge in the sky.  The pattern was eventually explained, and models were created which predicted (postdicted?) the patterns seen.  This explanation rests on the idea of inflation.

Conceptually, our universe is a bubble of "non-inflating" material slowly exuded by an enormous mass of "inflating" material around it.  Inflating material grows by a scale factor of $10^{38}$ every second and constantly generates non inflating material as a by-product, which condenses into universes like our own.  This means that our universe began life as a sub-atomic bubble and grew rapidly.  At that point, the scale of the universe was small enough that quantum field fluctuations were significant.  Because the growth was so rapid the state of these fields was essentially frozen for all time, leading to the non-homogeneous distribution of matter and Cosmic Microwave Background in the universe today (+).

So, like the coat of the tortoiseshell cat, the Cosmic Microwave Background captures an embryonic state allowing us to peer into the past.

• (*) After The Big Bang
• (+) Tegmark calls these bubbles "universes in the Level II multiverse".  In his nomenclature The Level III multiverse is the standard multiverse of the Many Worlds Interpretation.  It's interesting to note how the different interpretations of quantum physics would expain the non-homogeneity of the CMB.  An adherent of the MWI would say that every possible distribution of the CMB in the sky is equally real, but experienced in different parallel universes.  This sounds weird, but to my mind it is much less weird than Bohr's Copenhagen Interpretation which would have it that the CMB pattern was chosen at random when the wavefunction for the universe collapsed as a result of someone or something observing it.  Unfortunately the Copenhagen Interpretation doesn't help us identify who or what observed the universal wavefunction.  Perhaps it happened when the CMB radiation unevenly bathed the first unicellular life form!