The main issue: the third Meditation shows that God is not a deceiver because he's infinitely good.  But then, why does he allow me to come up with wrong judgments?
NOTE: This meditation as a mini-theodicy

1. Descartes opens with the point of having moved away from the senses and shown that God is better known than the mind and the mind better known than the body.
Problem: why is God better known than the mind?

2. Distinction between negation and privation, e.g., blindness in stone and man.  How my error involves the latter.  How can God allow this?
Two types of replies: i) based on an analysis of judgment; ii) based on divine inscrutability and the vastness of creation:

i) Judgment requires both understanding and will because it consists in the assent to an idea.  However,

• the understanding is finite, but is not the source of error.
• the will is infinite (it is the faculty which makes us most similar to God) and the source of error.
• error comes about when the will assents to what the understanding doesn't perceive clearly and distinctly.

So, error is our fault, not God's.  Nor can God be faulted for giving us an infinite will for:
• there is no deficiency in the will per se.
• the will is a simple infinite entity; it's all or nothing. Infinity comes with the package, as it were.
NOTE: Descartes views the will not as the last, or more forceful, desire, but as a faculty choosing among different desires and/or representations by the understanding. Contrast to Hobbes.
Problems:
1. What does it mean to say that the will is infinite and the understanding is not?  Presumably, that I cannot conceive of anything I cannot will. But I cannot will something which I can conceive as, and know to be, (even physically) impossible.
2. Does assenting to a proposition involve the will at all?  Don't I at times feel compelled to believe something I do not want to believe?
3. What are the criteria for perceiving something clearly and distinctly?
4. Moreover, as Descartes recognizes, God could have made me with the insurmountable inclination to assent only to what I perceive clearly and distinctly. He answers (4) by using (ii):

• his ends are inscrutable (hence, employing final causes is both useless and a sign of temerity in physics)
• the Big Picture theory (Augustine) shows that what seems evil from a small perspective may be good from a large perspective.

Meditation V: Of the essence of material things and God's existence.

Having discussed the mind, the task is now to discuss material things both with relation to their essence and their existence. The former task is taken up in Meditation V; the latter in Meditation VI.

1. Extension is the essence of matter because (Principles II, xi) conceptual analysis shows that all other properties (e.g., solidity, color, weight, temperature) can be taken away and still have a body (the wax). So, the essence of body is the same as that of space, tridimensional extension.

2. Ideas of extension, number, shape, etc. are innate because:

1. they are not factitious since they are independent of my will because:
• they contain implications which I did not foresee, and hence I did not put in these ideas. e.g. right triangle and Pythagorean theorem
• they contain implications which I cannot separate from these ideas, and hence are not dependent on my will.

Problem : onks; winged horses.
2. they are not adventitious, since some of the things represented in these ideas have not been experienced by me.
3. In reply to Gassendi, Descartes asks how I could recognize a crooked triangle drawn on paper as Euclid's triangle if I did not have its idea in me (human face example).

NOTE:  for Descartes, then, innate ideas are infinite in number.

• Innate idea of God and Descartes' version of the ontological argument: existence is part of the essence of God in the same way in which having the sum of internal angles equal to 180 degrees is in that of triangle.

Problem: is existence a perfection (property)?
Issue: Why is this proof here, rather than in Meditation III?
• Impossible to know anything perfectly without actually thinking of its proof if one does not know the existence of God as a being who is not a deceiver and on whom all things depend.

Problems:
• It is an extraordinary claim; presumably, the atheist geometer knows with as much certainty as the theist geometer
• Not clear whether it is an issue of memory or of change of eternal truths.

Meditation VI: On the existence of material things and the real distinction.

One can look at this Meditation as dealing primarily with 3 issues:
1) the existence of material things
2) the real distinction between mind and body
3) the relation between mind and body.

A. D. approaches the existence of material things in 3 stages:

First stage:
It is possible that they exist because Meditation V tells me that matter is extension, which I clearly and distinctly perceive (it is the  subject matter of geometry), and God can create anything I so perceive.
Second stage:
It is probable that they (in this case my body) exist because:

• I have imagination which
1. is very different from the understanding (myriagon example).

NOTE: the emphasis on this distinction separates rationalism and empiricism
2. is "a particular application of the mind to a body intimately present to it," presumably because imagination is strictly connected to the senses and is not an essential feature of my mind, since I can think of myself without imagination, and hence must be partially dependent on something else.

Problem:  how does he know that imagination doesn't depend on some accidental quality of his?
Reply: The argument is only probable. The best explanation for the existence of imagination is to suppose I have a body.
• I seem to have other faculties, e.g., the power of assuming various postures, which certainly presuppose having a body.

1. I find in myself a passive faculty of receiving ideas
2. the correspective active faculty is not in me since:
• I am essentially an intelligence, and such faculty does not presuppose intelligence (he has already proved the real distinction)

Problem: couldn't this faculty stem from a mental but accidental property
• These ideas appear independently of, and even contrary to, my will.

Issue: why doesn't Descartes use the faculty-awareness thesis?
3. Hence, this active faculty must be formally or eminently in another substance.
4. If it were eminently in another substance, then God would be a deceiver because:
• I have a great tendency to believe that it is in material things formally
• I have no faculty to recognize which beings would have it eminently aside from God.  But God could not be the cause of my ideas, otherwise I would be deceived.
5. So, this faculty is in material things formally.

NOTE: In sum, if material things were not the cause of my ideas of the external world, I would be deceived.
Problem: in view of Meditation I, I could remain skeptical and hence not be deceived.
Reply: God would not give me an instinct without the capacity to see it is unreliable, if it is unreliable.  It's true I have a tendency to believe that sensations are like the things they represent, but God has given me the capacity to know that this tendency is deceptive.

C. The real distinction: two things are really distinct if they can exist in separation.
Descartes' argument:
complete conceptual separability.   Mind and body can be thought is separation one from the other as an extended and a thinking thing; hence, they are conceptually separable; consequently, God can separate them in reality.
Problems:

• Arnauld's objection: right triangle and Pythagorean theorem (AT VII 78)

Descartes' reply: I conceive of mind apart from body as a complete thing.
Duplications:
What is a complete thing?
Do I have a clear and distinct idea of the mind qua intellect plus will as a complete thing? Role of the cogito?
• The real distinction is not sufficient to guarantee that the soul will survive the body

Reply: In the Med. Descartes is merely interested in establishing a necessary condition.  In the Synopsis he claims that the soul is naturally immortal because it (like the res extensa) is a substance, while the body is not.
• Even if one grants that the soul is naturally immortal, it doesn't follow that personal identity is preserved; compare with Locke.

E. The nature of consciousness:

• Indubitability of inner states when attentively attended to (Descartes admits that if distracted, we can take as clear and distinct an idea which is not).
• Transparency: if attentive, we cannot fail to be aware of an idea or a faculty in our mind.
• Consciousness is an all or nothing affair: having sensation involves having (some) understanding.

• Animals are mere machines and feel nothing for:
1. slippery slope generated by consciousness being an all or nothing thing: Do cats have a mind and hence are moral subjects? Do sponges?

NOTE: Leibniz on confusion and minute perceptions
2. animals are undeservedly horribly mistreated, and if they felt pain, then God would be unjust.
• Much of our own behavior is mechanical (breathing, digesting, walking without thinking about it, repetitive unthinking motion etc.).  However, humans are not (and presumably cannot be)  machines.  The three points in the Discourse:
1. animals cannot use language creatively.
2. animals have an ability to perform a limited set of tasks: reason as a universal instrument.

Problem: We could be merely tropistic minds with a rather complex program.  The sphex.
3. the very fact that some animals can perform one or two tasks with extraordinary ability and much better than humans, indicates that they are machines: the clock keeps the time better than we do.

G. The interaction and union between mind and body.
The interaction:
Mind and body interact: the mind causes changes in the body and the body causes changes in the mind.
Problem: How can matter, without having formally or eminently mental properties, cause mental events?

The nature of the union:
Christian philosophers pulled in two directions.  They want some separation of soul and body to guarantee immortality; however, they also tend to avoid saying that the soul uses the body merely as a tool (as a sailor might use his ship) because they must account for the appearance of union between mind and body.  Descartes tries to have it both ways:

1. the soul is distinct and different in nature from the body; however,
2. the mind/body relation is not like that of the pilot and his ship.  For, not only do they interact, but they do so in so intimate a fashion that there's a substantial union between soul and body (they are one thing potentially separable into two).  Two views of the union:
• natural institution theory: the mind is united to the body in so far God has instituted that certain modifications in the body (brain) correspond to certain modifications in the mind (God could have arranged things differently).

Problem: It would seem that because of the union there is a certain correspondence between bodily and mental states.
• Coextension theory: the mind is united to the body in so far as it is coextended with the body in being whole in the whole and whole in the parts, as in classical physics a moment of time is fully in each place and in the whole of space.

Problem: hard to see why coextension would explain union.

H. Conclusion.
If successful, the Meditations have achieved the following main results:
1) the establishment of metaphysical foundations for the new physical sciences. Matter is but extended substance, and hence subject to mathematical treatment on the basis of clear and distinct ideas of size, shape, etc.  Consequently, the physical world is like a big clock.  This leads Descartes to attempt mechanical explanation of physical phenomena, e.g. the explanation of the magnet.
Matter is put in motion by God.  Quantity of motion mv (scalar) is conserved because God is immutable and doesn't change the basic laws of nature.

2) the mind has been shown to be a substance independent of matter, and hence naturalism, the view that humans are fully explainable on the basis of the laws of nature, is false. However, tension set up by Descartes' attempt to explain many of the activities of man mechanically: the more this approach is successful, the more one is led to believe it could be extended to the mental.
There is one extended substance (nature) and a great number of unextended immaterial substances (minds).  Minds have free will and are outside of the mechanistic and deterministic material world in spite of interactionism.

3) hence the new science and traditional religious values (freedom of the will, immortality of the soul, existence of God, etc.) are not only compatible, but closely connected.