John 9 – Skeptic's Annotated Bible answered

1 And as Jesus passed by, he saw a man which was blind from his birth.

2 And his disciples asked him, saying, Master, who did sin, this man, or his parents, that he was born blind?

(9:1-3) "Who did sin, this man, or his parents, that he was born blind?"
The disciples ask Jesus about the cause of a man's blindness. Was it because he or his parents sinned? Jesus said neither had sinned. The man was born blind so that Jesus could show off his powers by curing him of his blindness.
Who makes people blind?

The author of the SAB contradicts himself here. In chapter 5:14 he claims that:

Jesus believes people are crippled by God as a punishment for sin.

But here he says that Jesus believed no such thing. So what is it?

3 Jesus answered, Neither hath this man sinned, nor his parents: but that the works of God should be made manifest in him.

4 I must work the works of him that sent me, while it is day: the night cometh, when no man can work.

BOM: 3 Nephi 27:32

5 As long as I am in the world, I am the light of the world.

6 When he had thus spoken, he spat on the ground, and made clay of the spittle, and he anointed the eyes of the blind man with the clay,

(9:6) "He spat on the ground, and made clay of the spittle."
Jesus spits on the ground, mixes his spit with the dirt, and rubs the muddy spit on (or in?) a blind man's eyes.
How did Jesus cure the blind man?

John Gill notes that making spittle was forbidden by the Jews:

"it is forbidden to put fasting spittle even on the eyelid on a sabbath day.''

It seems spittle was used to treat certain eye disorders. Probably not blindness... It was applied on the eyelids.
Calvin comments that as man was made from clay, so Christ uses here clay to signify that he who made man has the power to heal man.

7 And said unto him, Go, wash in the pool of Siloam, (which is by interpretation, Sent.) He went his way therefore, and washed, and came seeing.

(9:7) "Go, wash in the pool of Siloam."
A blind man's sight is restored by washing in the pool of Siloam.

Of course blindness cannot be cured by washing in some pool. As John Gill comments:

he did as he was commanded; he was obedient to the directions and orders of Christ, though they seemed so unlikely to answer the end; and yet that was brought about through the divine power of Christ, which appeared the more in making use of such unlikely means.

8 The neighbours therefore, and they which before had seen him that he was blind, said, Is not this he that sat and begged?

9 Some said, This is he: others said, He is like him: but he said, I am he.

10 Therefore said they unto him, How were thine eyes opened?

11 He answered and said, A man that is called Jesus made clay, and anointed mine eyes, and said unto me, Go to the pool of Siloam, and wash: and I went and washed, and I received sight.

12 Then said they unto him, Where is he? He said, I know not.

13 They brought to the Pharisees him that aforetime was blind.

14 And it was the sabbath day when Jesus made the clay, and opened his eyes.

15 Then again the Pharisees also asked him how he had received his sight. He said unto them, He put clay upon mine eyes, and I washed, and do see.

16 Therefore said some of the Pharisees, This man is not of God, because he keepeth not the sabbath day. Others said, How can a man that is a sinner do such miracles? And there was a division among them.

17 They say unto the blind man again, What sayest thou of him, that he hath opened thine eyes? He said, He is a prophet.

18 But the Jews did not believe concerning him, that he had been blind, and received his sight, until they called the parents of him that had received his sight.

19 And they asked them, saying, Is this your son, who ye say was born blind? how then doth he now see?

20 His parents answered them and said, We know that this is our son, and that he was born blind:

21 But by what means he now seeth, we know not; or who hath opened his eyes, we know not: he is of age; ask him: he shall speak for himself.

22 These words spake his parents, because they feared the Jews: for the Jews had agreed already, that if any man did confess that he was Christ, he should be put out of the synagogue.

23 Therefore said his parents, He is of age; ask him.

24 Then again called they the man that was blind, and said unto him, Give God the praise: we know that this man is a sinner.

25 He answered and said, Whether he be a sinner or no, I know not: one thing I know, that, whereas I was blind, now I see.

26 Then said they to him again, What did he to thee? how opened he thine eyes?

27 He answered them, I have told you already, and ye did not hear: wherefore would ye hear it again? will ye also be his disciples?

28 Then they reviled him, and said, Thou art his disciple; but we are Moses’ disciples.

29 We know that God spake unto Moses: as for this fellow, we know not from whence he is.

30 The man answered and said unto them, Why herein is a marvellous thing, that ye know not from whence he is, and yet he hath opened mine eyes.

31 Now we know that God heareth not sinners: but if any man be a worshipper of God, and doeth his will, him he heareth.

32 Since the world began was it not heard that any man opened the eyes of one that was born blind.

33 If this man were not of God, he could do nothing.

34 They answered and said unto him, Thou wast altogether born in sins, and dost thou teach us? And they cast him out.

35 Jesus heard that they had cast him out; and when he had found him, he said unto him, Dost thou believe on the Son of God?

36 He answered and said, Who is he, Lord, that I might believe on him?

37 And Jesus said unto him, Thou hast both seen him, and it is he that talketh with thee.

38 And he said, Lord, I believe. And he worshipped him.

39 And Jesus said, For judgment I am come into this world, that they which see not might see; and that they which see might be made blind.

(9:39) "For judgment I am come into this world."
Did Jesus come to judge people?
(9:39) "That they which see might be made blind."
So he came to make some people biind?

The author of the SAB missed the verse that looks most contrary to this one, namely chapter 3:17. But the meaning of the word judgment in this verse is a bit different from the usage mentioned in for example chapter 5:22 and chapter 8:15. This judgment is to be understood as a cause for an effect.
As those who look into the sun, become blind because of its exceeding brightness, so it happens to those we pride themselves in their own wisdom and who look at Christ. Christ is called the Light of the World (John 8:12). This light makes those who are blind to see, and those who can see, blind. So Christ is not the cause of the blindness, but blindness is the effect of Christ's like, see also 2 Cor. 4:4.
The words blind and see do not indicate something physical in this verse. There is no example where Christ makes a person actually blind. But it is an effect wrought in the mind. As Calvin explains:

But experience shows us the truth of this statement which Christ uttered; for we see many persons struck with giddiness and rage, for no other reason but because they cannot endure the rising of the Sun of righteousness.

40 And some of the Pharisees which were with him heard these words, and said unto him, Are we blind also?

41 Jesus said unto them, If ye were blind, ye should have no sin: but now ye say, We see; therefore your sin remaineth.