Ok, so I'm on the last chapter of 'Strangers to Ourselves'. I started reading this thread during Christmas, and like others mentioned, it actually made me depressed (Christmas didn't help). That is, the idea that we are nothing, or almost nothing, and that we are almost entirely controlled by mechanisms of which we know very little. That we are machines. Not that I didn't know that already - it just hit me.
I SEE you.
Hi Buddy. I understand what you mean with that phrase, and I appreciate it, so thank you!

However I also agree with what obyvatel and anart have told you. I'll add to what has been said that it seems to me that you are missing the point and escaping into some sort of baroque philosophical rationalization, when you should be feeling viscerally the horror of the human condition, as described by the psychological material, so that you can begin doing something about it.
I have also recently experienced a kind of visceral realization of the distinction between some Work ideas and the way the ideas are expressed by various people in varied contexts. With regard to 'being mechanical' or 'being biological machines', there is little reason to be sad about this. It just means we are thoroughly connected, on every level and scale, to Nature's ecology; and to our programming, we are naturally very responsive.
Sure, it is part of our nature to be mechanical; in a sense that is what makes us fit into this world. That is part of the General Law and that is why it is called like that. But remember that it is also within the laws of nature that creatures eat each other, predators are the norm and we all go back to dust and become fertilizer for trees, including the people you love the most. From this perspective, war with all its horror is 'natural', and so is psychopathy, torture, poverty, injustice, ignorance, etc.
The fact is that we have the unique opportunity of realizing that it is also possible to do things differently, through the so-called Law of Exception, which is nothing other than learning how to not be mechanical in order for good things to manifest through us: creativity, empathy, self-sacrifice, finding meaning to life, etc. So, if we have this chance, will we take it? Only if we viscerally feel that there is something wrong with being a predatory machine and/or food for predators.
Lately I've been thinking that what infects us with negativity and that bias towards 'negational identity' at times, are the cultural memes of people with profoundly limited awareness and a delusional state of mind. People who insist on their own indescribable importance all the time - and thinking that, because of this indescribable importance, every aspect of their being must also be indescribably important and not like mundane, inferior things at all. Oh no, they have no connection with the universe at all, do they?
In the real multi-verse, everything fits together. We live in a universe of cycles where there is no beginning and no end. In biology, we have the idea of plants feeding on fungus, insects feeding on plants, animals feeding on insects and fungus feeding on animals. No end; no beginning, so it's rather like fungus is the bottom and the top of the food chain at the same time. Even if it were not possible to achieve anything in terms of conscious evolution, I could be quite happy to be a thermodynamic or energetic equivalent of a fungus. It means I'm useful and needed. It's the very confined rigidity of those snooty azzhats that make them so limited in their usefulness to the universe, OSIT. 
Well, again, this perfect fitting-together of the universe that you describe is in one form or another true and good at the level of 'God'. But we are not God. We can contemplate the Big Universal Picture as much as we like, yet the fact is that God has placed us in this position of being machines, with the tiny possibility of making efforts to be something better than that. It is all fine to understand that from the point of view of God there is a purpose for everything, but this can also become an escape into avoiding making our own choices, living life and doing the Work. It is attempting to avoid our role in Creation - which come to think about it, is rather rude towards God, who after all placed us here so that we would play our parts one way or another. This avoidance is what Theodore Illion called the sin of trying to put oneself at the level of God (from 'Darkness Over Tibet').
Now you may tell me that this is not what you meant. That in fact you accept your role in Creation as a machine, or a thermodynamic fungus, as you put it. What strikes me then is, why are you so happy and calm about it? Wouldn't you rather be something different knowing that you may have the opportunity, as small as it may be? Illion also described this trap, and gave the example of people who were willing to give their food and even their lives and the lives of their children to rats, because they so much respected and loved rats as part of nature. This is another form of escape, one which leads to disastrous consequences, for obvious reasons.