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

Seldom have I seen anything more marvelous than watching the appropriate techniques “catch on” with someone who has suffered grievously from the effects of religious doubt. I have often said that the good feelings are not unlike watching someone come to the Lord. Fantastic blessings can be the result for those who learn and continually practice the biblical prescriptions, even when the situations looked so bleak at the beginning, and involved an exceptional amount of work. Two cases, in particular, come to my mind.

When Missy came to talk with me, she seemed to be suffering from more than the ordinary sort of emotional doubt. I sent her to a counseling clinic, where she was diagnosed with a potentially serious psychological disorder. She was treated with medicine and released. But she still had to deal with what she was telling herself concerning her salvation.

We met many times while she attempted to grasp the essentials of assurance. Many other painful things were going on in Missy’s life, too. There were multiple symptoms with which to deal. For several months there were ups and downs. Sometimes things were better, other times they were not. But she began to progress very slowly. The more she practiced, the stronger she got.

Due to the complicated nature of her situation, far beyond the emotional doubt alone, Missy needed some time to work everything through. At first, she failed to apply the principles in Philippians 4:6-9 in any consistent manner. But later it was these very precepts, in particular, that really changed her life.

The change has lasted for the long term, as well. Twelve years later, a few conversations showed that she no longer struggled with the issues that had dominated her life. She indicated that they were not even a factor. Although her path didn’t always travel straight upwards, and there were trials along the way, the trip ended with a fantastic victory. The principles she had learned affected more than just her doubt. They became beacons for her life, as she applied them to other subjects, too. Today, Missy is a missionary in Eastern Europe, sharing her testimony with other hurting people.

The second case came fairly early in my growing number of instruction sessions with doubters. It involved a graduate student, James, who repeatedly and sometimes rather belligerently charged God with not loving him. No amount of discussion would cause him to think otherwise. Some rather serious child abuse, along with some even more dangerous medical problems that altered moods, added much to his doubts.

We talked often about his questioning, but the meetings more often seemed to take the form of his challenging me to convince him that the biblical methods would work. Many a morning I would round the last corner to my office, only to find him sitting there without an appointment, wanting me to address his needs right then and there. Calls at home, or meeting me at sporting events for more discussions, were commonplace. But all during this time, James steadfastly refused to even try to apply the biblical principles. To this day, I have perhaps never seen a case where there was consistently so little effort in application. In short order, I was worn out!

One night James came to a college game to talk because he knew I would be there. I had finally had enough, and it had taken a long time for me to get to that place. I told him that he and I were going to duck into the first place we could find after the game ended. I was going to repeat the principles to him one more time, and if he didn’t make any more effort to apply them than he had done in the previous few weeks, we were done talking. That meeting after the game seemed to be the turning point! He was a very intelligent man and he certainly knew the proper responses to his doubt. Now he began to practice them. And he made very rapid progress.

Once, a few months later, James and I were having lunch and he was telling me how well he was doing. A young lady came over to our table and asked if she could sit and talk for a few minutes about her problems with doubt. Imagine my surprise when, before I could respond to the problem she had outlined, James held up his hand.

“May I handle this one?” he asked me. Dumbfounded, I wanted to see what he would say, realizing that I might have to jump in at any moment in order to rescue the woman from who-knew-what-kind of advice! But to my utter astonishment, James made a flawless case for beating emotional doubt! She walked away encouraged!

James’ changed life has also been proven over the long haul. He, too, had some tough times ahead, largely due to the outside factors mentioned above. In fact, he even needed surgery to correct some of the damage of the child abuse he had withstood. But fourteen years later, he is doing magnificently. There are no traces of the radical version of emotional doubt that had afflicted him. He just recently told me that it was all due to his finally beginning to practice principles like Paul’s in Philippians 4:6-9. He has since matured into a strong Christian leader, and is today pastoring a thriving church.

What else can we say? God changes the lives of those who practice His principles!

Why Do We Resist the Practice of God’s Truth?

Why did both Missy and James drag their heels so much when provided with a remedy to their emotional doubt? Both were suffering a significant amount of pain. Their problems were affecting every aspect of their lives. Doesn’t it seem that they would jump at the opportunity to get some relief? So why did they basically refuse to act, and for such a long time, too? For that matter, why does anyone fail to apply God’s truth when they have come to the end of themselves? There are few more intriguing sub-plots involved in this topic.

In my experience, the two most difficult points in the entire process of dealing with emotional doubt is discovering the falsehoods we tell ourselves and implementing God’s truth. It seems especially tough to do the latter precisely during the time in which we are most in need. These are the subjects for this chapter.

Of course, the bottom line for not applying truth is always the same: we prefer our ways to God’s ways. We more readily admit this in cases involving unbelievers (Romans 1:18-32). But we also saw in the last chapter that believers, too, struggle with disobeying God even after we know His will (James 4:1-10; 1 Peter 2:1-3).

Given that even believers ignore God’s teachings and disobey Him, why, more specifically, might a Christian fail to apply God’s directives concerning their emotional doubt, even when they are so obviously hurting? One reason it is difficult to pinpoint our unedifying thoughts in the first place is that doubters sometimes reject the view that they would ever lie to themselves at all. But the emotional doubter needs to face the fact that they are obviously telling themselves something that is out of whack, or they wouldn’t be experiencing the emotional difficulties in the first place!

God has forewarned us that it is very difficult to know our hearts and why we do the things we do (Jeremiah 17:9). It would seem that we are all candidates for misdirecting even ourselves.

A major justification for ignoring the untruths we tell ourselves is that some Christians think that there actually is some truth in their anxious thoughts. I hear this one quite frequently. “Well, didn’t I just flunk my big exam?” or “Isn’t it true that I was just diagnosed with a very serious illness?” When you hear it for the first time, this complaint really does sound like a show-stopper. What if the worst thing has just happened to them?

When truth is mixed along with the untruth, the doubting individual is often tempted to wonder if this procedure really works at all. This sort of case is more difficult to work through, but only because the person is less likely to see that they are still repeating untruths. And since the misbeliefs are present along with the truth, the former must be corrected if we are to achieve victory over our emotional questions. After all, it is the mistaken portion of the belief that causes the harm.

The hidden lies that often rear their heads in these circumstances are more devious, due to the fact that the negative things have already occurred. The misbeliefs sometimes abound: “Because of these horrible things, my life is forever ruined. I’ll never be the same.” Or, “My anxiety is completely justified, due to the hurt in my life. My circumstances have caused all of this.” Or, “The worst things possible have just happened to me.”

But our lives should not revolve around half-truths or temporary truths. Even though something has happened here, the unnoticed misbelief causes the anxiety. In cases like these, the half-truth hurts more than the outright lie.

Once after I had been lecturing on this subject, Chuck came up to me to talk. He had just lost his job and was in a state of turmoil. He discovered that he was more prone to question God’s goodness now. “How could God really love me?” Granted, this was a serious predicament for him and his family. But Chuck never realized that, while losing his job was definitely significant, it was also temporary. In no sense was it the worse thing that could possibly happen to him. Unfortunately, he told himself that it was just that: unbearable.

In situations like Chuck’s, it’s not the lost job that trips people up and causes the pain. If you still question this statement, then think about it: how can losing a job make us jump to the conclusion that God has done something to us, unless we’re drawing conclusions from the event? The problem is what we tell ourselves about losing the job: “I’ll probably never be happy again.” Or: “We’ll have to move and the kids will hate it.” Or: “Even if I do get a job, it’ll be for less money. We’ll have to change our lifestyle.” Or: “I won’t like the job as much, either.” After giving him a list like this one, I asked Chuck if he was saying things like these to himself. He admitted that he had been.

In other words, the chief obstacle with half-true statements is that the false portion will work on us, frequently causing anxious doubt. Like an undetected physical sickness, the lie stays hidden behind the truth until it is strong enough to produce some harm. Then it is much more troublesome to remove.

Still another reason that we fail to apply God’s truth to our doubt is that it may not be pleasant. Like pulling weeds, losing weight, or having a cavity filled, the final results might be quite nice, but we can never quite get around to performing the difficult procedure. Ridding our lives of doubt is admittedly not as simple as taking two aspirins and going to bed. God has told us that we must be willing to follow the instructions. Especially since the remedy is best applied during the problem (like medicine), this adds to the uncomfortable nature of the clean-up. Anxiety is tough enough on us itself without us having to do something else amid the turmoil. It’s like we’re crying out: “Just leave me alone with my worry!” We would rather procrastinate than face the music.

There are still other reasons that sometimes figure in when someone exhibits a problem with emotional doubt, but fails to join the program. Some just don’t get the point and, in spite of all indications to the contrary, still think that circumstances cause the emotions. Other doubters prefer the process of counseling more than they wish to be healed. Perhaps craving either attention or friendship, curing the uncertainty would effectively cut the water supply. Others cannot admit that they have a problem because that would militate against their sense of spiritual well-being or personal worth. It is far easier to deny the problem altogether or to place the blame elsewhere – probably on the offending events.

At any rate, there comes a time when doubters must make a choice. No one else can tackle their questioning for them. But the good news is that there is a remedy that works. As difficult as it may be for them, it just needs to be applied.

When Should We Practice?

Therefore, there is no substitute for practice. With all diligence, we should exchange our anxious doubts for God's glorious truths. God’s peace has been promised to us.

We have said that the most difficult instance in which to implement God's instructions is during the time of the doubting, since it sometimes takes an extraordinary effort to change subjects when our thinking is dominated by the painful dilemma itself. But this is also when we most need to apply one of God's strategies. It is precisely because we are changing the subject that the quandary subsides. It is like taking medicine: it might not taste good, but we require it most when we are sick. Like digging for splinters in a child’s hand, temporary pain is the way to gain lasting relief!

So the onset of the condition is the signal for action. Load the cannons and begin the assault! If healing and spiritual growth are desired, then we have to be willing to pay the price. Who knows? The solution may even be easier than expected, especially when some healing occurs. Like going home, when familiar territory comes into view, we are more willing to push ourselves.

I think the application comes much more easily to those who are willing to force their way doggedly toward the finish line. In this chapter, I’ve used examples from those who had lengthy healing processes. But it need not be that way. I’ve seen far more cases where the individual was almost completely healed of the more painful elements of their doubt by a concentrated application over a short period of time.

The chief idea here is to practice God's truths, and to do so particularly during the roughest times. The truth should be applied whether we feel like it or not. Paul tells us in Philippians 4:9 that rehearsing proper thinking until it becomes a habit is one of the keys to achieving peace.

We have already said that preventative therapy is also important. Like taking vitamins or participating in an exercise program, preparation ahead of time can be very helpful. As we get vaccinated during healthy times, so doubt prevention furnishes the necessary means to equip us for future needs, perhaps even keeping that rough time from coming altogether. Certainly, it often lessens the force of the emotional storm.

The main target for this strategy is those who know they have a tendency towards doubting. Remember that minimizing doubt is very helpful. Thinking through the options ahead of time allows us to greet the presence of questioning with the response, “Oh, you again. I’ve been waiting for you!”

What Should We Practice?

In the last two chapters, we concentrated on a number of cognitive practices that provided us with ammunition against doubt. Here we will provide some behavioral techniques that address Paul’s command to continually rehearse truth until it becomes a way of life (Philippians 4:9). Once again, the doubter may pick and choose methods that best meet their particular needs. Since each of the suggestions is biblical, applying any of them will be a positive step.

(1) Pray through the doubt. Paul (Philippians 4:6) and Peter (1 Peter 5:7) both command prayer during troubled times. Our petitions should be specific. While this is a great privilege, Scripture speaks of conditions for God’s answers. We are told to confess our sins beforehand (Psalms 66:18), to exercise faith (Mark 11:24; James 1:5-8), to be obedient to Him (John 15:7; 1 John 3:22), and to pray according to God’s will (1 John 5:14-15), and in Jesus’ name (John 14:13-14; 15:16). In ancient Israel, prayers sometimes went unanswered when God’s people lived in a state of unrepentant sin (Lamentations 3:42-44; Isaiah 57:11).

To turn the cognitive exercise of prayer into a behavioral one, several things could be done. We could write out our prayer requests, as well as the results. One helpful way is to list the specific requests in the left-hand margin, the results in a middle column, and any special notations on the right side of the sheet. Like Dana and his Sunday School Class in Chapter 7, this exercise could even be done with others. Answers would be an encouragement to faith and serve as a preventative against the common form of doubt that questions God’s involvement in our lives.

I kept a list of prayer requests and answers over a period of about two years. Approximately two out of three prayers were answered. Some of these were of the very difficult (even “impossible”) variety, and most of those received positive responses, too. Later, a seminary student told me that, like Dana, his Sunday School class also made a record of their classroom requests, and interestingly, they came up with a very similar result – about 70% of the prayers were answered.

We could also share with others in corporate prayer times, not only praying aloud, but rejoicing in the answers, too. I have often said that one of the main things I would emphasize if I ever returned to the pastorate would be to highlight the answers God sends, as well as the prayer requests. This is a tremendous encouragement to believers, but seems often to be neglected.

(2) Meditate through the doubt. Many times in Scripture, believers are told to meditate on God’s truth (about a dozen times in Psalm 119 alone). As opposed to the Eastern view of emptying the mind, biblical meditation is thinking deeply and single-mindedly on God’s truth. We’ve already mentioned briefly some examples of content in discussing Paul’s exhortation in Philippians 4:8.

Meditation is a wonderful avenue by which to both deal with particular cases of doubt, as well as practicing doubt prevention. During many of my years doubting, I made more use of this method than any other. Usually sitting on my porch on a dark, starry evening, I worked through various problematic issues, one by one. Usually, my chief methods were going through either Philippians 4:6-9 or Backus and Chapian's three stages, step by step. It’s a great way to think about God’s truth, as Paul commands.

But meditation can also be practiced corporately (Psalms 48:9). It can be a public exercise for believers who, together, concentrate on the Lord’s truths, perhaps centered around a certain theme. Strength could be drawn from the aspect of sharing these thoughts together.

(3) Worship through the doubt. We’ve discussed Paul’s exhortation to practice both thanksgiving for God's blessings and praise for His character. These two methods are especially helpful during times of uncertainty. Thanking and praising, in a very special way, liberate the believer to look beyond their immediate problems to God. It is very difficult to practice either one and yet remain engulfed in one's troubles.

A behavioral component can be easily constructed here. We could compose our own psalm unto the Lord. Whether or not you consider yourself a poet, share your deepest words of adoration with your God. Say them aloud. Or sit on your porch on a still morning during sunset and sing praises to God. What is your favorite hymn or praise chorus? Perhaps you would prefer to go for a walk and say or sing your words of praise.

Further, it is crucial to attend a Bible-believing church that takes worship seriously, where the emphasis is on meeting with God in fellowship with other of like mind. The corporate element adds a spark to our personal adoration.

(4) Memorize through the doubt. Take note of your most bothersome doubts. Which verses best apply to them? Write or type each text on a note card, arrange them in a meaningful order, and keep them together. Which biblical truths most apply to your misbeliefs? How can you think more clearly about them?

For years I carried with me everywhere I went a small container of business cards on which I wrote the truths that I most needed to be reminded of. I read them so much that the edge of every card was tattered and worn. I got tired of seeing the same things as I flipped through them, so I repeatedly told myself, “Yes, I know that.” But then my efforts against the doubts would stagnate. On one of the days when I thought I was making too little progress, I wrote across the bottom of one card: “If you know it, then do it!” I wanted more action! Less knowledge, more practice!

(5) Journal through the doubt. Keep a diary of your daily spiritual walk with the Lord. What doubts plagued you today? What things happened to you that you might have interpreted negatively, providing the stimulus for these thoughts? How did you respond to them? What methods worked? Which ones did not work so well? Could you have reacted in ways that would have been more profitable? What did you learn about God’s truth and its application?

Then periodically go back through previous days and see if you have made any progress. Do you notice any trends? Overall, do you find yourself returning to certain methods rather than others? Many believers have gained major insights into their walk with the Lord by taking the time to record thoughts and ideas like these.

(6) Recall through the doubt. Many biblical texts encourage believers to review past history in order to see what God has done (Psalms 105, 106, 114). In the last chapter, we suggested an exercise of picking a biblical hero or two who underwent doubt, in order to learn from his trials. As an additional exercise, make a list of their problems, their circumstances, how they responded, and how it turned out.

Another sort of recall is to count the answers to prayer that we have received over a specific period of time. Write them down. Meditate on the things God has done in your life. How many times have you triumphed due to His goodness? How does this show how He is active in your life today? During times when I have questioned God’s involvement, this method has never failed to be a ready antidote.

(7) Talk through the doubt. With emotional doubts, few things are as helpful as having a close friend or relative assist us in picking out our misbeliefs. Of course, the helper has to understand the “system,” so clue them in and watch this technique work. Loved ones often see the improper things we tell ourselves, even when we do not. Time and time again I’ve known the informed friend to notice what the doubter didn’t. Additionally, not only is the method readily available, but it can be a forceful change of subject, as we saw with Alexis in Chapter 8.

Wendy discovered that it was quite difficult for her to recognize her own distortions of the truth, since she had been believing these unedifying thoughts for so long. She frequently let things pass that she should have caught. Besides, it was hard to think that she would actually deceive herself. But on one occasion, her close friend Amber happened to ask her why she had just made a certain comment.

Recognizing that this was one of the things she had been working on, but had missed, Wendy explained the basic ideas of Philippians 4 to her roommate. After that, Amber began to help Wendy discover her falsehoods. Together they labored to weed out these untruths. Wendy even found a few of Amber’s problem areas, too!


Through all of our cognitive tools and behavior changes, we need to remember that victory rests chiefly on God’s power, weapons, and indwelling. Explaining our predicament to God and giving it over to Him, while at the same time expressing our faith in Him regardless of whether or not we obtain immediate answers, are moves in the right direction. They all help us to reaffirm our reliance on God, even when the way ahead is not clear. This is one way to strengthen our faith.

Unfortunately, when we believe our own lies, we also fail to look beyond our immediate circumstances. But temporal matters, even when truthful, are different from ultimate truth.

In contrast, Christians should be most concerned about ultimate truth (Matthew 6:19-34): we need to obey our Lord and lay up treasures in heaven, just like Jesus instructed us. One truth to continually drive home is that, even when Christians flunk big exams or think that God did not answer their prayer, they still have eternal life. They should view the present in light of their eternal future. If believers cannot appreciate the force of this, it could be because they have not really struggled with their salvation.

Here is the major point: Christians do not have to pass exams, keep their jobs, or even have the most successful prayer lives in order to be saved. Neither do they have to be the most popular, the best dressed, or the best athletes in the world. They don’t even have to be able to handle their doubt well! In fact, they do not have to do or be anything, except believers in Jesus Christ, in order to have the ultimate blessing of eternal life.

It is from this eternal perspective that all other problems should be viewed. Even death itself is not the definitive issue; that distinction belongs to the priority of God and His Kingdom (Matthew 6:33). This is the ultimate truth to be practiced.

Go to 9. Living With Questions

© 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).