(Sorry for the length)

Believing that life arose from the soup is no trivial matter. It is at odds with those people who believe that more than molecular mixing must have been at play. There are some tough cognitive steps, each a little harder than the next, that need to be resolved for such a conclusion to be reached. If you are one of those who is able to believe that life arose from the primordial soup, I admire your resolve, and ask you explain how you overcame these obstacles in the reply. In return I will lay out some of my case here.

The first cognitive step begins with what I assume is a bifurcation in thought and involves the electrostatic nature of the atoms that form into the molecules required for the soup. The atoms are finding each other and bonding in a spectacular variety of ways. The nature of this bonding property is important for what follows.

The wonder of this bonding action is trivialised in chemistry textbooks, yet it is akin to that part of the movie Terminator II when the metal from the shattered cyborg at the steel works melts and the melted blobs move toward each other and join together, forming larger and larger blobs, until the cyborg is reformed.

This blob formation- molecular bonding – is very strange. Covalent bonds, ionic bonds, ion-dipole bonds, dipole-dipole bonds, Van der Walls forces. They all cause conformational change in the molecules, so they bend certain ways – fold into certain structures. That atom's bonding properties are astonishing.
To not look at that interaction and wonder if there is something else we can’t quite account for beyond say filling the valence shell electrons, is interesting.

The second cognitive step that needs to be resolved is the creation of molecular machines out of these molecules. The enzymes that arise from carbon chemistry.

If I took you to my secret laboratory where I had a large tank of some fluid and into it in front of you I poured a satchel of a metallic powder-like substance and the powder began to bubble in the water and form itself into molecular machines, it would be very easy to suggest some type of design element had been engineered into the solution or the powder. The fact that believers in the soup are able to look at that and say, no, it’s just random luck, is a testament to their rock-solid faith that what they observe is not beyond the bounds of reasonable expectation. They say of course molecules will form that act as machines to catalyse reactions that otherwise may take millions of years to occur. But to me, it seems there is more to bonding then just bonding.

The third cognitive step is by far the biggest. What needs to be resolved is how these machines, having arisen through blind atomic bonding, then come to work cooperatively with each other in building the structure we call life. The person who can look at the nucleus of the cell and look past any temptation to see design is a credit to the theory.

To illustrate the point a little. DNA is a double helix – two strands wound around each other with base pairs bound to each other at the centre and holding the strands together. To copy or express what is inside the DNA, you need to pull it open (to rip it apart). There is an enzyme that does that called helicase. It undoes the hydrogen bonds between the bases. Of course it doesn’t do this all the time – only when copying is needed. Helicase in its turn is regulated. Once it has had its turn the DNA is sealed shut again by enzymes. An interesting accidental function.

After the DNA has been pulled open by helicase, copying is not straight forward. You need to know your start point. An enzyme called a polymerase has to attach with the aid of transcription factors to a region of the DNA called the promoter – after all, it would be pointless to start copying a gene from halfway through the sequence or halfway through the sequence of some other gene. A whole protein assemblage occurs at this point. As each new protein binds, resultant conformational changes to the quaternary structure move the process one step further to commencement of copying. Once everything is in place copying begins. See here for a simplified diagram

As the DNA opens for copying, it tightens rotationally at both ends (which are secured against the nucleolus), limiting its ability to open fully (imagine pulling open two strands of string wound around each other and tethered against each end – the more you pull it open the tighter the coiled resistance at the end becomes until you can’t open it anymore). There is an enzyme – topoisomerase, whose function it is to clip the tightening DNA strand and rotate it once, then reattach it again, so as to take the tightness out of the coil (how lucky was it that that randomly came into being).

As copying progresses along the DNA, because it is tethered at the ends there is another problem; the copying machine can’t go all the way to the end. Imagine a zipper that can’t fully run over the teeth of your zip because the end is closed. For this reason a section called the telomere has been attached. It is junk code at the ends of the DNA that allows the important genes to continue be copied by giving extra runway at each end- telomerase is an enzyme that actively adds this junk code in some organisms.

When the DNA code is being copied, the polymerase enzyme making the copy double checks it’s work. If it has mistakenly put the wrong base in, it backs up, takes out the wrong one, and puts in the correct one, then goes on about its business. This is called Proofreading (this enzyme is another fluke of random molecular mixing or copying errors).

But even Proofreading may sometimes not catch all mistakes, so there are a bunch of proteins called mismatch repair proteins whose job it is to check the finished work and make sure there are no mistakes, if a base has been mismatched, it will fix the mistake. So there is a double check in place.

Furthermore DNA damage can be fixed by chemical reversal, excision repair and double-stranded break repair, all mediated by enzymes: Not a double check, a triple check. This is an awful lot of spontaneously formed random molecular machines finding a critical role in DNA regulation where it just so happens that any copying errors could be disastrous to life. Any ordinary person when examining such complexity and control in other systems than biological would surely decide it had been designed.

There are many, many other proteins as well involved in DNA regulation and expression.

When we then realise that the proteins themselves are being encoded by the DNA, we have a quite intricate chicken and egg paradox. Was there simultaneity in the expression of the codes for the enzymes that would regulate the subsequent creation and expression of the DNA? How did the first copy happen? Were the first proteins encoded by DNA those needed to regulate encoding?- what a coincidence. And then what? It just started encoding other proteins that formed the intricate network of the cell, and all this happened through random mutation and copying errors which we have just seen are so tightly regulated? Holy Cow.

And I’m not outside the nucleus yet. So, I take my hat off to those of you who can look at this and only see a soup of randomness forming all the way into complex life. Your insight into this phenomenon or your faith is a lot stronger than mine.

I look forward to hearing everybody's position on the matter.