The Thomas Factor: Using Your Doubts to Draw Closer to God

A Christian friend of mine once had dinner with a world-renowned atheist. During the meal, the believer asked the philosopher if he had ever doubted his atheism. To his surprise, the friend told me later, the atheist responded basically like this: “Oh yes, I question the truth of my atheism all the time.”

Does this episode surprise you, too? Have you ever wondered why it is sometimes so difficult to believe? Have you ever thought that non-Christians have it so much easier because they have nothing to doubt (or to believe, either)? How about an even tougher question? Have you ever (privately, of course!) scared yourself with the (hopefully!) fleeting thought that it might even be preferable to be a non-believer, since this would uncomplicate your life?

We have said that the subject of doubt involves many twists and turns, including some that are very much unexpected. Some Christians might think that doubt only affects believers, while others may conclude that only non-Christians should fit this description. Yet, both are described in the New Testament by the term.

It seems to me after talking to doubters for more than twenty years, that there are strong reasons to think that virtually all Christians raise questions about God or their faith at some time. Only on two occasions have I ever heard a Christian deny that this was the case in their own lives. The first time I heard the comment was during a lecture given by a nationally known professor and author of dozens of books. (He had also written an article on the subject of doubt.) He insisted that he had never even once questioned God or his faith. The statement was made so firmly, and seemingly with full knowledge of the nature of doubt, that it haunted me for a few years. Later, the professor and I were alone for a meal and I brought the subject up again.

“Oh, you misunderstood me,” he explained. “I was only referring to not having certain types of questions. I often wonder why God does things the way he does or doesn’t, when it appears to me it should happen some other way!”

I had learned another lesson that day. Once again, this topic defied expectations.

The other time someone told me they had never doubted I had the opportunity to pursue the comment on the spot. The individual was the child of missionary parents and had been raised on the mission field. But after I spoke to her and to someone who knew her very well, the final response was that she had still never asked any such questions. While still somewhat skeptical of the assertion, even to this day, it is one more reason not to be overly dogmatic when speaking about what must always be the case.

Was it also true in biblical times that believers frequently experienced doubt of one sort or another? Did our heroes of the faith likewise struggle with some of these same issues? What about unbelievers – do they ever question their beliefs?

Old Testament examples

Throughout the Bible there are literally dozens of verses where true believers express their uncertainties, often in very strong terms. Several examples may be helpful in both illustrating points that we have already made, as well as in providing grounds for further lessons.

The Case of Job. The book of Job presents enough material for an entire chapter (or a book) on the expression of doubts concerning God, so we must be brief here. The basic story is a familiar one. God allowed Satan to test Job, a righteous man and his servant, to see if his faith was strong (1:6–12; 2:1–7). His sons and daughters were killed in a tornado-like storm. Most of his servants and livestock were killed by robbers. Job himself was in pain, inflicted over his entire body by sores (1:13–19; 2:7–8). Even his wife suggested that he give up his integrity, curse God, and then die (2:9). At first, Job remained firm: he accepted the calamity and praised God. He rejected his wife’s advice and refused to sin (1:21–22; 2:10).

But during the middle chapters of the book, in the portions that seem seldom to be read and digested, Job posed heart-rending questions about his suffering, even blaming God for it. He seemed to gain momentum as he went. He expressed what today would be called a death-wish, stating his preference to have died in childbirth (3:11; 10:18–19). Then he requested that God would slay him (6:8–9). He charged God with oppressing him while approving the actions of the wicked (10:3). Further, he said that God was watching him, just waiting for him to make a mistake (10:14). Then he demanded that God just leave him alone (10:20–21) and stop trying to frighten him (13:21)! After all, he thought that God had destroyed any hope that he might have (14:19).

In a major sub-theme, Job asserted his prerogative to complain (7:11) and even challenged God to a debate (13:3)! He thought that he had a right to state his case and have God reply (13:22). Job wanted to offer his arguments in order to justify himself (23:4–5). But, as far as Job was concerned, God had not spoken to him; he remained silent (19:7; 30:20) and denied him the justice that he was due (27:2).

Interestingly, Job was not punished for all of these accusations against the God of the universe, as far as we know. Although he had sinned (34:37), he also repented (40:3–5; 42:6). God honored his response and blessed him with far more than he had before (42:10–17).

Through all of this, Job learned some tremendous lessons that were exceptionally valuable. Although he never found out why he suffered, he learned a greater truth: he realized that he knew enough about God to trust him in those things that he did not understand (42:1–6). This information made him impregnable to the problem of why he suffered as he had. As long as he knew what he did about the nature of God, he also knew that there was a reason for the suffering, even if he did not know what it was. What greater lesson was there for him to learn? And it came at least partially through the doubt that he experienced.

The Case of Abraham. Next to Job, the best case of doubt in the Old Testament comes, paradoxically, from Abraham, whom Scripture calls a man of faith. In fact, perhaps no man in the Old Testament is better known for this attribute. Still, his trust in God did not come easily, and his struggles can assist us thousands of years later. Abraham learned to trust God, which would be a great lesson for us today.

Like Job, the general overview is well known. God spoke to Abraham (who was still called Abram) and told him to take his family and move from his homeland, traveling westward to the land of Canaan. He was given a special promise: a great nation would come from him in this new country and, through them, all the peoples of the earth would be blessed (Gen. 12:1–3). Abraham and his family obeyed the Lord and, after several incidents, settled in the land of Canaan, which God had given to him. He and his wife Sarah lived together for many years and later died in that country. God greatly blessed them and Abraham became the father of the Israelites through his son, Isaac, and his grandson, Jacob.

Many centuries later, the book of Hebrews showcased the life of Abraham. For the Jews, he was the most valuable player from a long history of stars. All of these accomplishments were won by faith in the God who called him. Abraham responded to God’s call and migrated to Canaan, even though he did not know where he was going (Heb. 11:8–10). Later, he believed God's promise that he and Sarah would have a child, even though there were two huge roadblocks: both of them were well beyond child bearing years, and Sarah was childless. But because Abraham believed that God was trustworthy, he became the father of a great nation (11:11–12).

Further, Abraham was even willing to sacrifice his own son Isaac, the child of promise, again because he believed God and trusted him. God would raise Isaac from the dead if he had to do it that way (11:17–19). James captured the chief idea like this: Abraham lived his life by faith and God honored and blessed him (Jas. 2:21–24).

At this point, we might wonder what’s the point of all of this. The history lesson is nice, you might think, but how can we really relate to Abraham? That’s tougher than trying to hit a home run just because we know that Babe Ruth was able to hit so many!

And didn’t Abraham have advantages that we, frankly, never have? Didn’t God speak directly to him? Couldn’t Abraham continue to talk directly to God whenever he wanted to do so? Didn’t God always respond? Those were simply far different times from today, right? It cannot be the same for us.

But if we go back and examine the texts more closely, we may find something quite different. What if Abraham also struggled with the question of God's silence? What if he didn’t hear from God on a regular basis? What if he, too, needed assurance that God was at work in his life?

For instance, at the close of Genesis 16, Abraham was 86 years old (16:16). As far as we are told, God didn’t speak to him until 13 years later when Abraham was 99 years old (Gen. 17:1)! We cannot be dogmatic here, but it is at least possible that God did not communicate with Abraham during these years. From the other chapters, it doesn’t seem that God conversed with Abraham on a weekly or even a yearly basis during the rest of his life, either. There may have been sizeable gaps. Wouldn’t most Christians today even say that God had communicated with them more than once in the last 13 years?

Yes, Abraham was certainly a man of great faith. And God did speak to him, although perhaps not anywhere near as much as what we might have thought. But this did not keep Abraham from asking God for the assurance of his promises. How could he be certain that Canaan would be given to him (Gen. 15:8)? The Lord allowed him to know this truth by the use of a supernatural manifestation in order to make a covenant with Abraham (15:13–21). Faith does not exclude asking good questions and receiving good answers!

Yet, all of this – God’s call and supernatural revelation – did not keep Abraham from undergoing several troublesome moments. Like Job, Abraham also struggled with his faith. On two occasions, Abraham purposely concealed the identity of Sarah in order to save his own life (12:10–20; 20:1–18). But we have to answer a tough question here: if Abraham really believed that God would raise up a great nation from him, why should he be so fearful for his life, as the texts tell us (12:12–13; 20:11)?

Then when Sarah still hadn't conceived the promised child, she convinced Abraham to bear a son (Ishmael) by her servant Hagar, in spite of God's promises (16:1–16). It seemed like she wanted to help God along. Yet, Abraham agreed with her. Then when the Lord repeated the promise that Sarah would bear a child, Abraham literally laughed at God (17:15–17), as Sarah did later (18:10–15)! Where was that faith that made him so famous?

It would be wrong to malign Abraham's faith. These episodes were spread over twenty five years (cf. Gen. 12:4 with 21:5), and that provides many chances for slip-ups. No one has lived a perfectly consistent life except our Lord Jesus Christ. Overall, Abraham acted in faith, and never allowed unbelief to master him. Besides, we should understand Abraham very well. Haven’t we ever acted similarly, perhaps by attempting to rationalize our faith and help God along? We say, “Maybe what God really meant was …” We can understand Abraham and be encouraged by his actions precisely because, just like us, he failed several times. We can relate to that!

How did Abraham overcome his doubts regarding God's promises? Paul used Abraham as his example, in spite of these momentary lapses. When he could have walked away and ignored God's call, Abraham chose to believe instead. When he was promised a child, he did not disbelieve, even though all the medical data opposed it. Rather than give up or cease to believe, Abraham’s faith was actually strengthened (Rom. 4:18–25). So here we find one of his secrets: Abraham not only exercised his faith, but it grew as he trusted God more and more, one step at a time, even after several failures.

Imagine having a faith that grows when life’s pressures are at their peak! Yet that was Abraham's experience. Like Job, the primary reason for this is that he concluded that God was trustworthy: what he already knew about God was enough to trust him in unknown areas (Rom. 4:20–21). New steps were taken, based on what had already transpired. Abraham trusted God and was strengthened even during the toughest of times.

Other Texts. Another Old Testament book that contains open, honest questioning by believers is the Psalms. Like Job, one theme is also that of evil. Several psalms charge God with allowing the wicked to enjoy life (like 74:1), while the righteousness of the godly gained them nothing but punishment (73:12–14). It is said that God defended and showed favoritism towards the wicked (Ps. 82:2). These sorts of doubts are found elsewhere, too (Jer. 12:1–2; 15:18).

A second theme, as with both Job and Abraham, concerned God’s silence. David complained that his prayers went unanswered (35:13–14). Then, after sinning, he cried out to God to restore the assurance of his salvation, like he had once experienced it (Ps. 51:8–12). The Jews declared that they had not heard from God in quite a while (74:9). This idea also occurs in other Old Testament books (Lam. 3:44; Isa. 57:11; 59:2). In Daniel 10:10–14, one of the prophet’s prayer requests had been delayed for three weeks by an attack on God’s angelic messenger by what appears to be demonic forces!

Perhaps the strongest complaints about God from a single text occur in Psalms 44. The writer, in very strong language, rebuked God for not fulfilling his promises even though Israel had done nothing wrong (44:17–26; cf. 89:38–39). Then, in a simply startling statement, the writer even blamed the God of the universe with sleeping on the job (44:23)!

A last example of God’s silence occurs at the close of the Old Testament. Before the birth of Jesus Christ, about four hundred years passed without a canonical prophet or book. Of course, this does not mean that God was not at work. But like the comment in Psalm 74:9, many may have wondered how long it would be before the Lord officially spoke. Was God angry with his people? Had he cast them away and rejected them? Was he done giving the inspired Scriptures? Would no prophet come forward and speak for him? When would the silence end?

Another verse in the book of Psalms may give a little hint. Just as the darkest of nights is still followed by a new sunrise (Ps. 30:5), so the Jewish “dark ages” were officially ended when the Messiah entered human history, to die and rise in order to offer redemption to the world. What an incredible end to the Old Testament! God’s profound silence was broken by the most splendid turn of events in all of history.

New Testament examples

Although much shorter and with significantly less narrative than its counterpart, the New Testament also presents some major cases of doubting believers. We can also learn from these examples.

In a startling but frequently overlooked text, while John the Baptist was in prison, he sent two of his disciples to Jesus. John had a question or two: was Jesus the Messiah or should John be looking for someone else (Matt. 11:1–11; Lk. 7:18–30)! On the surface, at least, wouldn’t this seem like an unnerving question to ask the Son of God? “Are you the true Messiah? If you aren’t, we may as well follow this other rabbi over here.”

It’s not just the question itself that’s so staggering. If it came from someone in the crowd, it would probably be dismissed by many readers as being from someone who lacked faith. What turns it into such a bombshell is because it comes from John the Baptist, God’s chosen forerunner for Jesus, predicted in the Old Testament (Isa. 40:1–3). Was John in danger of throwing his faith overboard?

First, let’s note Jesus’ immediate response. He didn’t react in a vindictive fashion, such as by telling John to shape up, or to live up to his reputation, or by quoting verses to him and reminding him of his special position as the chosen herald of the Lord’s coming. Neither did he, as some Christians would suggest, ignore evidences that might address John’s need. Rather, he cured a number of suffering people right there in front of the two messengers and then instructed them to go tell John what they just witnessed. Apparently, Jesus thought that there was some relevance between his healing miracles and John’s faith. That is a lesson in itself.

But the story doesn’t stop there. Notice a second development. As the two visitors left, Jesus addressed the crowd concerning John. He asked them if, when they went out in the wilderness to see John, they had expected to see someone who was easily shaken by the wind (somewhat reminiscent of James’ warning about weak faith in Jas. 1:6–8). Or did they see a weakling in soft, comfortable clothes? Then Jesus told his listeners that John was not only a prophet, but he proclaimed that no greater man had ever been born! What makes this even more incredible is that John hadn’t yet received Jesus’ message, so Jesus was complementing John while he was still doubting! And while there was no rebuke for his lack of faith, Jesus did instruct John not to be offended because of him (Matt. 11:6; Lk. 7:23). I take this to be like an encouragement that we often give someone today: “Hang in there! Don’t give up.”

I hesitate to mention another case from the Gospels, for fear that there be some misunderstanding. But what do we do with Jesus’ distress in the Garden of Gethsemane? We are told that his mental suffering was so intense that he was sweating drops of blood (Lk. 22:39–44; cf. Mk. 14:33–36; Matt. 26:36–43). This signals an exceptional amount of strain. Jesus prayed to his Father and requested that the coming events be bypassed, but only if it was God’s will. Certainly the portion of the prayer relating to God’s will was accomplished, but what about Jesus’ earlier request?

It is very difficult to address this incident. Taking the texts in a straightforward manner, Jesus undeniably suffered emotional anguish, brought about by the questions that he faced. We may agree that here is an example where Jesus encountered some of the same problems we face, yet without sinning (Heb. 4:15). We might even say that this was one of the times where we are told that Jesus learned obedience by his suffering (Heb. 5:8). That is why believers today can identify with him. He personally experienced the reality of emotional pain.

The case of "Doubting Thomas" (Jn. 20:24–29) is probably the best known example of uncertainty in the New Testament. Thomas wanted to see the risen Jesus with his own eyes before he would believe. Although Jesus did provide the requested evidence, He also issued a mild rebuke to his apostle. It would have been better if Thomas had believed the testimony of the other apostles who reported to him that they had seen Jesus alive (Jn. 20:29), the same witness that we read in the New Testament. Once again, Jesus does not shy away from using evidence to answer doubts, but he didn’t think that Thomas’ version – a direct appearance – was the most desirable option. Besides Jesus’ prayer to his Father in Gethsemane, Paul specifically tells us that he prayed on three occasions concerning the removal of an apparent physical problem. Some think that he had problems with his eyes. After all, didn’t he need to be healthy in order to minister? But Paul was not answered as he had hoped (II Cor. 12:7–10). He learned what Jesus already knew, that God’s will was to be preferred above one’s own. What about unbelievers? In more than one place, we are told that they asked questions, too. Paul says that Jews ask for signs (I Cor. 1:22–23). Jesus rebuked those who wanted proof that he was from God (Matt. 12:38–45; 16:1–4). He offered his miracles to other Jews who accused him of making them doubt by not telling them who he was, but they refused to believe anyway (Jn. 10:24–26, 37–39). He even healed a boy whose father confessed: “I do believe; help me overcome my unbelief” (Mk. 9:24).


Before we return to our task of deciphering the maze of Christian doubt, we need to pause long enough to point out some lessons that come strictly from the texts that we have just discussed. We can learn from the experiences of believers who have traveled this path before us.

(1) As we have already said in our opening discussion, doubt is multi-faceted. This should be even more obvious after a brief survey of its expression in the Scriptures. The presence of evil and the issue of God’s silence are two of the most common types. Assurance is another key issue, whether concerning the certainty of truth or of one’s own salvation. Other saints struggled with God’s guidance and his promises, especially as it impacted their expectations. At any rate, it is helpful just to see some of the various manifestations of this widespread phenomenon.

(2) Some doubt is rebuked, as in the cases of Job and Thomas. And God honors repentance, as with Job. But not all doubt is reprimanded, and not all questions are deemed to be sinful (Abraham, Paul). Neither does doubt keep a person from being complimented for his righteousness (John the Baptist).

What about especially strong expressions of doubt that are uncensored, like Psalm 44? It seems that the Holy Spirit allowed the honest expression of feelings by true believers, even when it was not always appropriate or true. But this is certainly not an excuse for us to try the same thing, or to blame God for whatever happens to us. Honest, unpremeditated questions are one thing; constant preoccupation with strong statements that question God’s character may indicate something else altogether.

(3) Believers like Job, Abraham, and Paul grew during their times of doubt, even when their faith underwent the harshest attacks. Today, too, while uncertainty can certainly have negative results to be avoided, it can also help us to learn some indispensable lessons. Perhaps the main issue here is what Christians do about their struggles: to whom do we turn and what is our attitude towards what is happening? What applications do we make?

(4) One lesson is so crucial that it deserves mention by itself. Believers like Job and Abraham learned that God could, indeed, be trusted, even when they couldn’t figure everything out. They discovered that they already knew enough about God in order to have confidence in him in those things that they didn’t know or understand.

Sometimes we, too, just need to trust him more, in light of this truth. Few lessons are more valuable for us today, since we know far more than did these Old Testament saints. Just to be sure that Jesus Christ died on the cross for our sins and rose again from the dead should make us willing to trust him in times when we don’t understand why things are happening as they are. After all, we don’t have to figure out everything in order to know that these truths ensure heaven, where we will understand! This approach needs to be generously applied to all of our struggles.

(5) Many times in Scripture, doubt is simply expressed without any remedy being provided. But when relief does come, we get some hints about what helped to bring the comfort. While the use of evidences is not the remedy in most cases, it is certainly one of the most frequent means of treating doubt and was employed when appropriate. Abraham received a sign of God’s blessing, while John the Baptist’s disciples presumably told him about Jesus’ miracles. The risen Jesus appeared to Thomas. Other methods were also helpful. The psalmists suggested praise even when their circumstances hadn’t changed yet (Ps. 35:27–28; 89:52). Another recommendation was to remember and proclaim what God had already done in history (Ps. 105–106; Lam. 3:21–26). Job found comfort through dialogue. David and Paul discovered consolation in God’s truth.

(6) Concerning unbelievers, it appears that Jesus treated differently the various requests he received for a sign. John the Baptist wasn’t rebuked, while Thomas received a mild admonishment, but neither was refused. On the other hand, the unbelieving Jews were strongly chided after they demanded a sign, although they were told that Jesus’ resurrection would be a sign in their case, too (Matt. 12:39; 16:4). What was the distinction? Why were some shown miracles and others were denied? It seems that Jesus differentiated between his listeners, based on the state of their heart. The strongest reprimand was reserved for those who were closed to his work, no matter what he did.

But it cannot be said that he reserved his miracles for believers only. Not only did he heal the man’s son after the former’s confession of partial unbelief (Mk. 9:24), but it could even be argued that Thomas was not a Christian when he demanded to see the resurrected Jesus. Not only did Thomas refuse to believe the resurrection until Jesus appeared to him (and this event is an indispensable part of the gospel – I Cor. 15:3–4), but Jesus said that Thomas believed only after seeing him (Jn. 20:25, 29). Lastly, as we mentioned, Jesus said that the sign of the resurrection would still be given even to the staunchest of his skeptics (Matt. 12:39; 16:4).

So the fact remains that some of Jesus’ unbelieving hearers had doubts, too, and frequently severe ones. Today, as well, skeptics tell us that they have asked very similar questions. We saw this in the opening lines of this chapter.

Another example is provided by C.S. Lewis, who was an ardent atheist during his early teaching at Oxford University. He confessed that he sometimes experienced doubts about his faith after he became a Christian. But, he added, in the days when he was an atheist, there were times when the Christian faith appeared to be "terribly probable." No matter what you believe, Lewis says, you will doubt at some time. The more important matter is, how will you deal with the doubt when it comes? (Mere Christianity, Macmillan, 1952, pp 123–124).

These statements by Lewis provide the opportunity for a reassessment of some of our earlier comments. Sure, Christians can certainly have some rough times. God has certainly not promised us anything different. Yet, how would it be to walk a mile in the atheist’s shoes? How would you like to be an unbeliever and secretly fear that Christianity may, in fact, be true? How long would it take you to move from that thought to the petrifying realization that Hell might just await you?

In the passages we looked at, Scripture plainly reveals the presence of doubt in the lives of believers and unbelievers alike. Why should we think that unbelievers are exempt from religious uncertainty? People doubt for a very basic reason – all of us are human beings and we share a sin nature. This is the root cause of our uncertainty. In other words, our sinful human nature is the state from which all of this questioning springs. But this is not to say that all doubt is necessarily sin.

Randy was a believer who kept his questions concerning his faith to himself. But the more he did so, the more they bothered him. He never heard the subject discussed in sermons, so he concluded that very few Christians struggled with it. One day when it seemed to nag him a little more than usual, he took a chance and dropped some hints to a knowledgeable friend. It would be an understatement to say that Randy was surprised to find that it could be a very normal problem, and that even his friend was not exempt! Further, when his friend turned to one Scripture passage after another to illustrate his point, Randy grew more and more relieved. Just to know that other Christians struggled with this subject seemed to relieve much of his concern.

We conclude that religious doubt is very common and affects almost everyone at some time. It is not necessarily sin, nor must it be the opposite of faith. It can even produce some good results. But it can also lead to serious situations that need to be treated. Along the way, however, there are many misconceptions concerning this topic. It just seems that doubt has an image problem!

Go to Chapter 2: "Common Myths"

© 1999 Gary R. Habermas
Please note that some of these chapters have been slightly edited for use on
The Thomas Factor: Using Your Doubts to Draw Closer to God by Professor Gary R. Habermas was originally published by Broadman & Holman: Nashville, TN (1999).