We know all we need to know about the quantum field theories upon which chemistry and biology are based because of the physical structure of the universe and of these systems. This is the property of 'decoupling' in effective field theory descriptions of a physical system, such as in the noted Appelquist-Carazzone decoupling theorem.

In modern language you can think about this as follows. Let's say you have a physical theory whose degrees of freedom are characterized by different energy scales $E_{+}/E_{-}\gg 1$. The 'high-energy' modes $E_+$ and the low-energy modes $E_-$ have some generic interactions amongst themselves and with each other.

You can do what's known as integrate out the 'heavy' or 'fast' or 'high-energy' modes with energies around $E_{+}.$ This means you remove them from your theory entirely, to produce a theory which only includes the degrees of freedom with energies around $E_{-}$.

And yet there is an equivalent description of your system including only the physics of 'light' or 'slow' or 'low-energy' degrees of freedom which has the same structure but now only contains the $E_-$ degrees of freedom and their interactions amongst each other! You just need slightly different values for their energies and couplings and such than if you used a description with the $E_+$ degrees of freedom included as well.

This comes to bear on your question because chemistry consists of processes characterized by electronic binding energies, which are $E_{-} \sim \rm \alpha^2 m_e \sim {\rm eV}$ with the fine-structure constant of QED and the electron mass. In these processes in fact all you need is non-relativistic QED, because $\alpha^2 m_e \ll m_e$ and you don't care about the existence of positrons when you're doing chemistry. You certainly don't need to know about the fact that the proton is a composite of the strong force at a scale $\Lambda_{\rm QCD} \gg m_e$, or that the electron is actually chiral and it gets its mass from the Higgs boson at a scale $v_{\rm EW} \gg y_e v_{\rm EW} = m_e$.

So there is a theory of molecular biology which should be understood perfectly well in terms of which nuclei are present and what their atomic structures are. For example, there is no dependence on what physics looks like beyond the Standard Model. Indeed, this is why it's so hard to experimentally determine what particle physics is like at smaller distances---if you aren't going to very high energies, then you need to look for effects which are either incredibly small or incredibly rare. Your theory of molecular biology cares not a whit for their existence.

I agree it does not, but we can be more precise about why, physically this is the case.

We know all we need to know about the quantum field theories upon which chemistry and biology are based because of the physical structure of the universe and of these systems. This is the property of 'decoupling' in effective field theory descriptions of a physical system, such as in the noted Appelquist-Carazzone decoupling theorem.

In modern language you can think about this as follows. Let's say you have a physical theory whose degrees of freedom are characterized by different energy scales $E_{+}/E_{-}\gg 1$. The 'high-energy' modes $E_+$ and the low-energy modes $E_-$ have some generic interactions amongst themselves and with each other.

You can do what's known as integrate out the 'heavy' or 'fast' or 'high-energy' modes with energies around $E_{+}.$ This means you remove them from your theory entirely, to produce a theory which only includes the degrees of freedom with energies around $E_{-}$.

And yet there is an equivalent description of your system including only the physics of 'light' or 'slow' or 'low-energy' degrees of freedom which has the same structure but now only contains the $E_-$ degrees of freedom and their interactions amongst each other! You just need slightly different values for their energies and couplings and such than if you used a description with the $E_+$ degrees of freedom included as well.

This comes to bear on your question because chemistry consists of processes characterized by electronic binding energies, which are $E_{-} \sim \rm \alpha^2 m_e \sim {\rm eV}$ with the fine-structure constant of QED and the electron mass. In these processes in fact all you need is non-relativistic QED, because $\alpha^2 m_e \ll m_e$ and you don't care about the existence of positrons when you're doing chemistry. You certainly don't need to know about the fact that the proton is a composite of the strong force at a scale $\Lambda_{\rm QCD} \gg m_e$, or that the electron is actually chiral and it gets its mass from the Higgs boson at a scale $v_{\rm EW} \gg y_e v_{\rm EW} = m_e$.

So there is a theory of molecular biology which should be understood perfectly well in terms of which nuclei are present and what their atomic structures are. For example, there is no dependence on what physics looks like beyond the Standard Model. Indeed, this is why it's so hard to experimentally determine what particle physics is like at smaller distances---if you aren't going to very high energies, then you need to look for effects which are either incredibly small or incredibly rare. Your theory of molecular biology cares not a whit for their existence.