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

Emotional doubt can sometimes lead to dire consequences. Or it can help to produce believers who are vibrant and growing. It all depends on our response to it.

When Jennifer first called, she was a bit combative. Having read my earlier book on doubt, she wanted to argue about what kind of uncertainty she was experiencing. I listened to her description of the problem. Then I asked the same questions that we’ve discussed throughout this book.

“Don’t tell me it’s emotional,” she responded.

“Why not?” I countered, sure that this was the nature of her unrest. “What would be wrong with that?”

“I just have an image in my mind of men in white coats,” she answered.

It took a while to work through that misconception. Then, after realizing that I was probably correct in my identification, she issued her next challenge.

“And don’t tell me to just pray and be spiritual. Everyone tells me that,” she sputtered.

Over several lengthy phone calls, I understood more of where she was coming from. Fitting the description of the typical high powered executive, Jennifer was a Vice President in a large corporation. A good thinker with good people-skills, she was moving quickly up the ladder. A single woman and a believer with a strong family background, she also possessed a fine grasp of Christian truth. But somehow her faith and her business skills were not working out. It was her faith that was suffering. She had prayed to trust Christ literally hundreds of times, but somehow she still questioned her salvation so thoroughly that she didn’t even consider herself to be a believer.

After many talks, including speaking at length about Philippians 4:6-9, she decided not to pursue a remedy for her doubt. Somehow, she just wasn’t ready to apply the procedure. “I’m going to let it go for a little while and see what happens,” she reported.

About three years later, she called back. I was quite surprised to hear from her, given the way she had called off the earlier discussions. At the time, I had felt like a salesman who couldn’t close the deal!

In the meantime, she had changed jobs and, as judged by the business world, she was a raging success. But her private world was crumbling around her.

“My boss would think I was going nuts if he knew what I was calling about. He thinks I’m at the top of my career, but I’m completely miserable. What I most want, I can’t have,” she complained. “I don’t care about money or success. I only want the Lord, but I don’t think He wants me. It’s affecting everything I do. I have to do something about it.”

Jennifer’s uncertainty had affected negatively every aspect of her life, including her business and her personal life. She testified that not a day went by that it didn’t cause her exceptional grief. When she began the second round of calls, she told me that she had been brought to an all-time low point. She had a choice of either turning to the Lord or watching her life fall apart due to questioning her relationship with the Lord. This time around, she did not even question the identification of her struggles as emotional. She knew it to be the case.

Over the next few months we talked regularly, making a weekly appointment for a call. Jennifer started very slowly, still exceptionally leery of applying the biblical steps, or even admitting that they would be helpful at all. But once she began, she went at it tenaciously. The walls of emotional doubt crumbled around her very quickly, given the depth of her inner turmoil.

Jennifer developed into a textbook case of what can happen once the application of biblical principles takes place. In the next few months, she began to grow in her walk with the Lord. Having attended a biblical church all of her life, she had always been a worker. In the days to come, she began leading a woman’s Bible study, as well as talking to other women about their struggles with emotional doubt. In my twenty-five years of giving advice on this subject, I’ve very seldom seen this drastic a change. But the Lord turned everything around when she decided to get serious in the application of His principles.

We saw similar patterns in earlier chapters. Missy found that even suffering from a psychological disorder did not keep her from gaining victory over her need for assurance (Chapter 9). James decided that the only way to conquer the severe childhood hurt in his life was to make the decision to apply biblical precepts (Chapter 9). Ken’s changed perspective on the nature of theology led to a corresponding modification of his views on Christianity as a whole (Chapter 10). All three had changed from believers whose questioning dominated their lives. As the old saying goes, doubt can either make you or break you.

Negative Consequences

Throughout this volume we have seen examples of changed lives that have come as a result of dealing with religious doubt. Yet, many persons suffered significantly until they made the decision to change. We’ve also seen some cases where people chose not to do anything about their doubt, accepting those consequences, as well.

In this chapter, we will look first at five unfortunate consequences to which religious doubt can lead. While there may be some overlap here, each presents a different angle on the problem. Notice the progression between the stages of reaction. Doubt frequently moves similarly.

(1) Doubt often leads to a degrading view of God. The doubter almost always thinks that God has in some way abandoned him or her, or otherwise hurt them in some way. After all, shouldn’t God, who can do anything, want to help us to feel better? Then why don’t I have more peace and less pain? Somehow, it is surmised that God is at fault here. He must not care about me or want to help. This generally makes the emotional situation even worse, pushing the individual further from God and His truth.

Sadly, the bad theology keeps the sufferer from pursuing the truth: his own faulty thinking has produced this situation. As we have seen over and over again, our doubt arises, not from the circumstances around us, but from the things we tell ourselves about what happens. So not only is the doubter suffering, but he or she is likely compounding the uncertainty with bad thoughts about God.

(2) Bad theology often encourages bad habits. The murkiness moves further. Habits like thanklessness also develop. When children learn traits like this one, adults are quick to point out: “You kids would complain even if you got every last thing you wanted.” Or, “Children are so ungrateful. I wished I got everything you have when I was small.”

But as adults, are we any more thankful? We respond: “Well, that’s different, I didn’t get everything I wanted.” How dissimilar is this? We are just as quick to blame God for all of our frustration and even our shortcomings!

Cynicism develops, too. Once we’ve crossed the line to blaming God, everything can be laid at His doorstep. How convenient! We are no longer responsible for our thoughts and actions. God is supposed to kiss it and make it all better! If He doesn’t do so, He’s obviously let us down. Sometimes we sneer at thoughts about Him. But if an answer to prayer is sandwiched in there some place, God is a Hero again. We can be such fickle people!

We could go on and continue to name more bad habits. But these are sufficient to make our point. Bad theology affects our attitudes. More seriously, sometimes there is no recovery from unthankfulness and especially cynicism. Once these attitudes are ingrained deeply into our psyches, it’s hard to remove them. Did you ever start to really not like someone and notice what happens whenever you see them? Even when they’re doing something positive, it’s too late. Once we label someone a loser, it takes a lot to change that designation. It’s just a short step to despising them. And when believers who suffer from this sort of doubt hear about God, they can begin to despise Him, too, if they are not careful.

(3) Bad theology and poor attitudes affect our motivation. Why should someone follow God when they think that He has wronged them? And what if He doesn’t care about us at all? Does that make us want to follow Him more?

When a believer loses his or her will to continue on the heavenly path, passivity sets in, like spiritual rigor mortis. Suffering a reversal of direction in our commitment to God can similarly be devastating. How do you get a dead person to move? There’s the problem! It’s so difficult to move what is no longer in motion toward a goal.

(4) Now we reach the flip side of apathy. When we don’t think and do the things we should, we lose momentum. Sometimes it’s easier to do the things we shouldn’t. Sin always seems like an easier move. Sin is also contagious. One sin often leads to another.

Maybe the person will keep the flood gates from opening – maybe they won’t. But once we’ve crossed the line and let our defenses down, it is so much easier to do it again. Most of us know the feeling that comes when, after losing weight and gaining most of it back again, we reach a place where we feel like we really don’t care whether or not we eat every cake and bowl of ice cream in the world! At that point, short of a major change of direction, we’ve lost the battle.

I will always remember one person who came to talk. While passing through the area, Lee came to see me about her doubt. A college graduate and a believer, she was concerned about her motivation to follow the Lord. She determined that she was lagging in her commitment to the Lord, due to the presence of regular sin in her life. But try as I might, she was no longer willing to turn to God. I will always remember the end of the meeting, knowing that nothing had changed and that she would not repent and commit herself to Him. It was a chilling departure that afternoon.

(5) The most serious of the repercussions of religious doubt comes to the one who seemingly abandons all or part of their faith and hardens their heart against the Lord. Sometimes this comes as a result of a long struggle that started as factual questioning, moving on to emotional issues. Old wounds yield scars and perhaps a “Who cares?” attitude. It follows for many that if God isn’t on my side, why should I have anything to do with Him?

This sort of believer has continued down his or her path and refused to benefit from all the many blessings of the Christian faith. Their decision comes in spite of all the evidences for faith, the emotional remedies provided by wonderfully healing texts like Philippians 4:6-9, and the possibility of victorious living in light of eternal life.

What are the possible signs that may indicate that someone is in danger? This is an exceptionally difficult question because we can never be sure of another’s heart, or when someone has crossed the line. Neither should we presume to announce our opinions to or about such persons. But due to the seriousness of the situation, and out of sensitivity to our suffering brother or sister, we might still venture a humble, cautious response.

Perhaps the clearest indication is that the person is no longer thinking, acting, and talking in a biblical manner, or in keeping with their previous commitment. Maybe references to the Lord bring sneers or derogatory remarks. Or their own language about God may betray them – especially if it is flippant or callous. Another possible indication is the inability to make spiritual decisions. Like Israel, perhaps there is an insensitivity to spiritual things, as the writer of Hebrews warns (Hebrews 3:1-15). Possibly there is a lack of fruit in their lives (Matthew 7:18-23; Hebrews 6:7-8). They have probably abandoned Christian fellowship (Hebrews 10:25).

What characteristics are necessary in the spiritual counselor? Sensitivity is absolutely required. The person must first be sensitive to the Lord, then to the hurting individual. The latter must never be given an excuse to think that we are responding for any reason other than out of love and concern for God, His Word, and them. Humility is also an essential. There must be absolutely no sign of haughtiness or arrogance, which are condemned by our Lord (Luke 18:9-14). Pray for discernment in these matters, for much may depend on the words of the adviser. Boldness may even be necessary here, if the situation demands it. The potential that a brother or sister in Christ may be in danger outweighs one’s personal desire not to be involved in the situation.

How should the concerned person respond? What steps might be taken? Where do we begin? The best place to start is with ourselves. Spend time with the Lord in prayer. We need to search our own hearts in order to test our motives. Why are we getting involved? Is there any desire whatsoever just to meddle in someone else’s life or see if we can uncover some tidbit about them? Do we feel like we “owe” them one? What about our own relationship to the Lord? Have we examined ourselves (1 Corinthians 10:12; 11:31)? Have we repented of all known sins? As far as we know, is there anything between us and the Lord or between us and another believer?

Next, seek the advice of mature Christians. This is not a decision that should be made lightly, or by the judgment of a single individual. Pray together and seek the Lord’s will. Pray for the leading and intervention of the Holy Spirit. The work is His.

When meeting with the doubter, listen to his or her concerns. Ask good questions. Where are they now with the Lord? Be aware of any progression of the doubt. At what stage does it seem to be? Are they sensitive to the Lord? In what areas? How do they respond to the overall situation? Are they concerned? Remorseful? Where do they think their doubt might take them if they pursue their present course of action? Do you agree with their assessment? If necessary, be prepared to confront them lovingly, but firmly.

Some believers who are otherwise close to a serious problem may still respond, due to the work of the Holy Spirit. They may also be touched by your love and show of concern. If they are open to assistance, begin by suggesting repentance.

Then be prepared to suggest appropriate biblical steps that address the particular issue. We have made many such suggestions. Assist them in applying these principles or make immediate arrangements to do so. Regular follow-up and fellowship are also necessary.

Steve was a college graduate, a very committed Christian, and a very intelligent young man who was well versed in philosophy and apologetics. But a few of his close friends told me that he had recently become an agnostic while finishing his Ph.D. I called Steve one night and asked him about his shift of allegiance. Imagine my surprise when he admitted that what I had heard about his agnosticism was true!

We had several lengthy conversations during which he admitted the chief reason for his change, which was not factual, but a problem with sin. As is very common, he had concluded that those who would point out his problem were themselves the difficulty. It was almost as if he thought that rejecting his faith would still his conscience (and the convicting of the Holy Spirit).

I was firm in my comments, while still trying to speak in a compassionate manner. Convicted, he repented a couple of discussions later. I also addressed a few philosophical questions. Dave seemed serious about his return to the Lord. In fact, even a few years later when we talked again, he was holding fast to Christian theism.

Positive Consequences

Emotional doubt can also be the instigator that brings about positive results in the believer's life. We will list here seven of these advantageous side-effects in the hope that such will encourage the individual to both work on their uncertainty and continue to mature in their Christian walk, in spite of their questions.

(1) Initially, we may learn how to study and discover answers for ourselves. Especially with factual questions, few habits are more useful or gratifying for their own sake. Some report that this is one of the most gratifying results of tangling with their religious quandary. This knowledge should be helpful in future situations or in assisting others who have similar questions.

(2) Having worked through uncertainty, we grow as persons. Some researchers have even concluded that we do not grow as individuals unless we experience doubts and personally labor through various sorts of questions.

(3) We learn that emotions are not our enemies. Contrary to the impression given by some researchers, emotions are not bad. They are God-given. Think of all the fantastic memories and other experiences that are ours because of this wonderful gift from God. More than this, we have seen that these same emotions can be trained to behave! They can be brought into agreement with our thinking. Why not have the best of both gifts? This is a key emphasis in this book.

(4) In addition to achieving a new appreciation for our emotions, thinking properly also teaches us to love the life that God has given to us. Personal conflict helps us to appreciate existence without the problems. The only time pain feels good is when it subsides and finally stops. When we struggle with doubt, we value a life where the questioning has calmed down enough so that we can stop and smell the roses.

(5) Emotional doubt extends an extra, rather shocking benefit. Some doubters talk about their doubt as an “It,” a monster that grips them with fear at its every bidding. It chases and pursues them, scaring them almost to death. But additional reflection shows that this is certainly not the case. Rather than being some sort of ogre that sneaks up on us and attacks, our emotions are obviously part of us. And we want the best for ourselves, don’t we? So our feelings are like guard dogs, sitting by our side and watching out for us! They are not growling at us, but at the bad, unedifying thoughts that are approaching up the walkway towards us, as well as the ones we have already invited into our lives!

So emotions are spiritual alarm clocks, buzzing loudly when we are entertaining thoughts that we have no business contemplating. We may not like being awakened in the morning from a blissful sleep, but we’re still happy for the availability of a wake-up call. This is what our emotions do for us. They are our alarm clock that sounds off when we cross the line into unedifying territory. We simply misinterpret its blessings, thinking we’re being attacked! Chalk up one more misbelief on the subject.

Upon reflection, Terry discovered that her unwanted emotions were not evidence of her having "fallen away" from Christianity or some other dastardly thing. Rather, she surprised herself by discovering that her feelings occurred precisely because she had entertained thoughts that were contrary to her Christian beliefs. So she decided to make the most of her passions. Learning to relax whenever the feelings popped up, she allowed her emotions to become an early warning system, sounding off whenever she began to think in a non-biblical manner! This was her signal to begin one of the biblical strategies that she found so helpful. The fear subsided substantially.

So the emotions that we thought were so negative have taken yet another ironic twist. Our feelings are on our side. They support our struggles. In a strange sort of way, God has spoken to us through them!

(6) Not to miss the forest for the trees, the experience of doubt can actually lead to its own death! By dealing properly with our emotions, we can quiet at least the most painful side-effects of such questioning, as well. Assurance and peace can actually be its conclusion (Philippians 4:7, 9).

In other words, learning to apply God’s truth to our emotional struggles of all types, our feelings can be trained in all its aspects. The application can be made in such a way that we learn to deal with all emotional matters, including emotional doubt, teaching us how to manage our most trying times in life.

When my doubt reached the emotional stage, it came on with such fury that all my cannons had to be trained specifically on the painful elements in order to get any relief. But when the smoke cleared away and I learned to control the feelings, I realized an even more wonderful truth. The emotional species of doubt that had plagued me for so many years could be handled in roughly the same way. How many unforeseen twists were there to this topic? Doubt certainly was not everything it was supposed to be! And most of the revelations were positive, too.

(7) Lastly, doubt helps our faith to mature. Our new thinking should contribute to a deeper spirituality. We should come away from these trying times of uncertainty with a deeper desire to come to know better the God whose truth we believe. In this sense, Christian growth is taking place.

Having actually grown in the midst of our suffering, thankfulness and praise to God are the natural results. We develop a new appreciation for how He works in our life. Just like Job, although we may have started out by questioning Him, we may end up actually being a living example of just how God works such a process out. How many ironies can come from this one subject? Paul calls us God’s workmanship (Ephesians 2:10) and adds that God will finish the work He has begun in us (Philippians 1:6). Being obedient through the process of doubt can aid in that process.

Dealing with emotional doubt has taken us to the practice of biblical disciplines like prayer, thanksgiving, praise, meditation, and personal study. In working through our questioning, we may have been pursuing the path of increased spirituality without even realizing it. The last thing we should do is stop this process of growth when our pain begins to subside. This is the very time we should be increasing our spiritual progress, not only as preventative therapy, but also as a means of continued growth.

The resulting maturation continues to push us in the direction of practicing the other Christian disciplines, too. If, with the Psalmist, we desire God and long for Him with all of our hearts, then we should seek Him (Psalms 42:1-2). We can pursue those practices that can increase our intimacy and fellowship with Him.

Some may now ask a great question that has perhaps been building throughout the book. Since religious doubt produces so many positive consequences, why do we emphasize corrective thinking and try to change the feelings?

Such healing is needed for at least three reasons. First, we have also seen that, perhaps because of the many surprises on this topic, believers draw many false conclusions. But failing to deal with doubt in the correct manner can also lead to serious harm. We would like to stop this sort of problem before it gets a chance to develop. Second, the emotional element is frequently so painful that the person at least feels like they need immediate treatment. It is normal for human beings to want to avoid pain, even if it produces some positive results. Third, the benefits that come from doubt generally come only after the uncertainty is treated. The blessings, then, are largely manifest only in retrospect.


Over a period of 25 years, I have dealt with approximately 100 individual cases of doubting persons, keeping records on almost every one of them. The vast majority of these (about three quarters), both male and female, were emotional in nature. About three quarters of the total were followed up in subsequent talks, with well over half of these coming more than one full year later. I have had long-term contacts over the years with more than one-third of these persons.

The vast majority of individuals improved significantly. Almost without any exceptions, the emotional doubters, in particular, reported marked improvement, as judged by their own testimony. Since I never charged anyone or otherwise received pay from any of them, all they had to do if they were still hurting was to contact me again. As part of a very unofficial survey, their satisfaction was judged primarily by their follow-up testimony to me, but also by their not returning beyond the last contact, even though I always left that option open. This would seem to be a fair, twofold indication of a decent amount of ongoing contentment.

The bad news is that some refuse to follow biblical instructions. Rejecting God’s warnings and failing to follow His recipe for peace, they continue in their pain and uncertainty. Often, they blame God and / or their circumstances, when their chief problem is what they tell themselves and how they respond to what happens.

In contrast, the great news is that emotional doubt is usually treatable. We may have victory through God's power, weapons, and the indwelling of the Holy Spirit. It is an added benefit of God's grace that something seemingly so painful and otherwise negative may be turned around (often quite quickly) to produce so many positive effects.

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© 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).