In part 1, I dealt with problems and concerned raised by the study itself and the data it used. In this section I will present ideas that counter the overall conclusions atheist draw from the study, namely that atheism must be true because it's believed by more intelligent people. The first argument that I present is about the lack of longitudinal data.
The researchers of IQ are measuring either per-college or college students. Not too many of these studies measure IQ's of middle aged adults. They are getting them at a time in their lives when they are either beginning to want to leave home or when they have left home for the first time. Francis says the shock of the "atheist professor" is not as great as it used to be:
The long discussed shock of freshmen encountering Atheistic professors at college and the transition problems from childhood beliefs to intellectually defensible beliefs have been reduced in recent years. Today the shock comes earlier and with less force than in decades past.".Nevertheless, they are still free from the parents for the first time. They are striking out in independence for the first time. Now its time to rebel and experiment and throw off the chains of parental oppression. Few if any of these studies follow them through life to determine if they became believers latter in life. This is a real possibility that they will. Studies show that people become more religious as they age. McCullough et al found that "results were consistent with the rational choice theory of religious involvement." The Zuckerman study found that the negative correlation was stronger in collage age than before college. So this is a good indication that perhaps its the college years when people experiment and the more intelligent are more likely to reject for a time what their parents taught them then they will come back to it latter in life when they are more mature. The Atheist IQ studies, which are not so much done by atheists per se as used by them, are not good predictors of what intelligent people really think. They really only predict the extremes that intelligent people go to during extreme parts of their lives.
There is dissatisfaction with the conventional IQ test as a measure of intelligence.For example "Richard Nisbest psychologist from University of Michigan, Ann Arbor, difference in IQ scores largely disappear when researchers control for social and economic factors." David Shenk argues that the standard Stanford-Binet test only measures a variety of skills and thus is an indicator of academic progress. They are designed statistically to keep in same place in the pack but they are not indicators of intelligence.
A big myth about IQ is that the scores can't change over time. IQ scores do change over time. IQ scores "can change quite dramatically as a result of changes in family environment (Clarke, 1976; Svendsen, 1982), work environment (Kohn and Schooler, 1978), historical environment (Flynn, 1987), styles of parenting (Baumrind, 1967; Dornbusch, 1987), and, most especially, shifts in level of schooling," according to Cornell University's Stephen Ceci.  IQ scores do not imply a fixed or inate intelligence, Shenk quotes Ceci, "There is plenty of evidence, for example, that schooling raises overall academic intelligence."  Shenk goes on to ask:But did this stability prove that the tests revealed innate intelligence?Far from it. The reality is that students performing at the top of the class in 4th grade tend to be the same students performing at the top of the class in 12th grade, due to many factors that tend to remain stable in students' lives: family, lifestyle, resources, etc.Being branded with a low IQ at a young age, in other words, is like being born poor. Due to family circumstances and the mechanisms of society, most people born poor will remain poor throughout their lives. But that doesn't mean anyone is *innately* poor or destined to be poor; there is always potential for any poor person to become rich.The happy reality is that IQ scores:A) measure developed skills, not native intelligence.B) can change dramatically.C) don't say anything about a person's intellectual limits. 
Don't genes limit our intelligence? Isn't intelligence "heritable?" his answer is:
No, and no. Very sloppy science and journalism has led us to believe that what scientists call "heritability" (derived from twin studies) is the same thing as what we ordinary folk call "heredity." In fact, they are not even remotely the same thing. Genes certainly do have an impact on intelligence, and everyone has their own theoretical limits, but every indication is that most of us don't come close to our true intellectual potential.He links to another article, by himself, "The Genius in All of us."
Nesbsit sums up his study of the latest findings:
We review new findings and new theoretical developments
in the field of intelligence. New findings include the follow-
ing: (a) Heritability of IQ varies significantly by social
class. (b) Almost no genetic polymorphisms have been
discovered that are consistently associated with variation
in IQ in the normal range. (c) Much has been learned
about the biological underpinnings of intelligence. (d)
“Crystallized” and “fluid” IQ are quite different aspects of
intelligence at both the behavioral and biological levels.
(e) The importance of the environment for IQ is established
by the 12-point to 18-point increase in IQ when children
are adopted from working-class to middle-class homes. (f)
Even when improvements in IQ produced by the most
effective early childhood interventions fail to persist, there
can be very marked effects on academic achievement and
life outcomes. (g) In most developed countries studied,
gains on IQ tests have continued, and they are beginning in
the developing world. (h) Sex differences in aspects of
intelligence are due partly to identifiable biological factors
and partly to socialization factors. (i) The IQ gap between
Blacks and Whites has been reduced by 0.33 SD in recent
years. We report theorizing concerning (a) the relationship
between working memory and intelligence, (b) the appar-
ent contradiction between strong heritability effects on IQ
and strong secular effects on IQ, (c) whether a general
intelligence factor could arise from initially largely inde-
pendent cognitive skills, (d) the relation between self-reg-
ulation and cognitive skills, and (e) the effects of stress on
One of the major disproofs of the validity of IQ tests is a phenomenon known as the "Flynn effect." This is a disproof becuase it indicates that IQ not fixed, it rises with time and that what is being measured is actually not intelligence but cultural literacy.
Multiple studies have documented significant IQ gains over time, a phenomenon labeled the Flynn effect. Data from 20 industrialized nations show massive IQ gains over time, most notably in culturally reduced tests like the Raven's Progressive Matrices. To our knowledge, however, this is the first study to document the Flynn effect in a rural area of a developing country. Data for this project were collected during two large studies in Embu, Kenya, in 1984 and 1998. Results strongly support a Flynn effect over this 14-year period, with the most significant gains found in Raven's matrices. Previously hypothesized explanations (e.g., improved nutrition; increased environmental complexity; and family, parental, school, and methodological factors) for the Flynn effect are evaluated for their relevance in this community, and other potential factors are reviewed. The hypotheses that resonate best with our findings are those related to parents' literacy, family structure, and children's nutrition and health.Flynn argues that our ancestors were not dumber. He rules out better nutrition or knowing the tests better. The bias of the test is such that a kind of technological imperialism is imposed upon the masses.
Flynn cites a hypothetical, but typical, test question: “How are rabbits and dogs alike?” Answers such as “both destroy gardens,” “both are dinner in some countries and pets in others,” or “you can use dogs to hunt rabbits” are true, but the response the IQ testers want is “both are mammals.” The question tests not knowledge of the world or of functional relationships but mastery of particular abstract concepts, which the test makers have themselves internalized as trained scientific professionals and literate intellectuals.
The tests reward problem solving that reflects a bias toward the technological sort of thinking.
IQ tests also reward certain problem- solving abilities—what Flynn calls “problems not solvable by mechanical application of a learned method.” He cites tests of similarities and analogies, and pattern-completion tests, such as Raven’s Progressive Matrices. In the latter, each question is a series of line drawings followed by a collection of drawings from which the test taker must pick the one that completes the sequence. When J. C. Raven developed the test in 1936, he claimed it measured the ability to discover patterns, which was for him the essence of intelligence. Raven’s test is often said (without good evidence) to suffer little or no cultural bias. Yet it is on tests of this type that the Flynn effect is strongest; gains in IQ scores of at least 5 points per decade have been seen. In the Netherlands, for decades all 18-year-old males drafted into the military were given the test, and those who took it in 1982 scored 20 points higher than those who had taken it in 1952.Some have asked "if IQ tests are not predicting intelligence, or at least not fixed, unalterably, heritable standard of intelligence, what do they predict?" The Flynn effect give us one answer, cultural literacy. Another answer is academic motivation. That is not necessarily a marker for intelligence, since a bright student can be turned off from the process of learning or trying. Angela Lee Duckworth, a psychologist at the University of Pennsylvania, and her team, conducted two studies; they did a meta analysis of 46 previous studies, the effect of monetary incentive's on IQ scores."...the effect of financial rewards on IQ scores increased dramatically the higher the reward: Thus rewards higher than $10 produced g values of more than 1.6 (roughly equivalent to more than 20 IQ points), whereas rewards of less than $1 were only one-tenth as effective."
Duckworth's second study involved data from an earlier study, following 500 boys age 12, tested in the late 80s, they were video tapes and signs of boredom and lack of motivation were observed. The study was longitudinal, following the boys into early adulthood. There were no difference in IQ or other factors bewteen the boys.
Duckworth's team analyzed the results of these earlier studies to see what they said about the relationship between motivation, IQ scores, and life success. By constructing a series of computer models of the data, the team found that higher motivation accounted for a significant amount of the differences in IQ scores and also in how well IQ predicted later success in life. For example, differences in motivation levels accounted for up to 84% of the differences between the boys in how many years of school they had completed or whether they had been able to find a job. On the other hand, motivation differences accounted for about only 25% of the differences in how well they had done in school as teenagers. According to the researchers, that suggests that native intelligence does still play an important role in both IQ scores and academic achievement.
Nevertheless, the Duckworth team concludes that IQ tests are measuring much more than just raw intelligence--they also measure how badly subjects want to succeed both on the test and later in life. Yet Duckworth and her colleagues caution that motivation isn't everything: The lower role for motivation in academic achievement, they write, suggests that "earning a high IQ score requires high intelligence in addition to high motivation."
This finding of course raises the question does this mean that those with high intelligence will score low on the test if they are not motivated? That test scores fluctuate at different times in your life would seem to be proof that IQ doesn't measure a fixed unalterable course. Take a book reviewed by NYT book review in 1998, published by Brookings Institue, the work shows that test scores between black and white narrow only a bit since 1970 but "the typical American black still scores below 75 percent of American whites on most standardized tests. On some tests the typical American black scores below more than 85 percent of whites?" Yet no genetic aspect has ever been discovered that would indicate that blacks are any less intelligent than whites. As a matter of fact when black children are raised in white homes their per-adolescent test scores rise dramatically (that also goes for mixed race children). Black adoptee test scores fall in adolescents.  I would actually predict that, since at that time the difference in racial make up of the family becomes more acute (I base that upon the experience of relatives). That could be a motivational issue. Moreover, the findings reported above by Nisbet shows the IQ gap bewteen blacks and whites has narrowed a lot more since 98.
--Even nonverbal IQ scores are sensitive to environmental change. Scores on nonverbal IQ tests have risen dramatically throughout the world since the 1930s. The average white scored higher on the Stanford-Binet in 1978 than 82 percent of whites who took the test in 1932. Such findings reinforce the implications of adoption studies: large environmental changes can have a large impact on test performance.
--Black-white differences in academic achievement have also narrowed throughout the twentieth century. The best trend data come from the National Assessment of Educational Progress (NAEP), which has been testing seventeen-year-olds since 1971 and has repeated many of the same items year after year. Figure 1-2 shows that the black-white reading gap narrowed from 1.25 standard deviations in 1971 to 0.69 standard deviations in 1996. The math gap fell from 1.33 to 0.89 standard deviations. When Min-Hsiung Huang and Robert Hauser analyzed vocabulary scores for adults born between 1909 and 1969, the black-white gap also narrowed by half.
Some scientists attribute the difference in IQ between men and women to motivation. Males surpass females by average of 3.6 IQ pionts, but more males decide to go to college than females. William and Mary psychologist Bruce Bracken thinks this is a good argument for linking motivation to the test score. 
The question is if IQ is really measuring motivation, what are atheists motivated toward? Why would those who don't believe in God have a greater motivation than those who do? Let's not forget the idea that IQ tests are also measuring sort of "cultural literacy," or we might call it "indoctrination." People who score higher on IQ tests are those who have more successfully indoctrinated into the ideology of scientism, since that seems to be the dominate force in the culture. That tallies with findings I've discussed on AW about atheists low self esteem. Leslie Francis produced the correlation between rejection religion in youth and low self esteem. There is a voluminous data consisting of many studies already on the issue of negative God image and the relation it bears to self esteem. It seems that negative self esteem is connected to negative God image.
Persons with high levels of self esteem may find it difficult to share the same religious belief. A theology predicated upon a loving accepting God is cognitively compatible with high self esteem, but it could be a source of discomfort for a believer low in self esteem. It does not make good cognitive sense to be loved when one is unlovable. Consequently the latter person can march to a different theology, one that is more consistent with his self image. (Benson and Spilka 209-210).
If we put together the two explainations, cultural indoctrination into an ideology of technique (scientism), with the idea that IQ represents motivation, what are the atheist's motivated to do but to excel at the culturally prescribed ideology as a means of bolstering self esteem? Since they reject God based upon self esteem, they connected the bolster (scoring well on tests as a mark mastery over the culturally prescribed ideology) as an alternative to belief. Thus they are initially spurred by aversion to belief based upon low self esteem (if you don't like yourself why would you like the one who created you to be the way you are?) the means of bolstering self esteem is to replace the creator with a process of accident then mastering the understanding of that process to show one's worth. If religious are more inclined to accept personal experience of life as a clue to ultimate reality and the meaning of their lives then they are not as motivated to excel in mastery of an ideology, or at least not that ideology, but to seek more truth on a personal level that can't be subjected to such tests.
 Francis, L. J. . "The relationship between intelligence and religiosity among 15-16 year olds."
Mental Health, Religion and Culture (1998) 1,185-196. doi:10.1080/13674679808406508, 188,
 Michel E. Mcullough, Craig K. Enders, Sharon Brion, Andrea R. Jain, "the varieties of religious development in adult hood: A longitudinal investigation of religion and rational choice."
Journal of Personality and Social Psychology. the American Psychological Association(2005, Vol. 89, No. 1, ) 78–8, 78.
 Zuckerman, et al, Op. Cit. (see part 1) from the study Abstract, 1.
 Michael Balter, "What Does IQ Really Measure?" Science Now, (4/25/11)
 David Shenk, "the truth about IQ," The Atlantic, (July 28, 2009), http://www.theatlantic.com/national/archive/2009/07/the-truth-about-iq/22260/
David Shenk is the author of six books, including Data Smog ("indispensable"—The New York Times), The Immortal Game ("superb"—The Wall Street Journal), and the bestselling The Forgetting ("a remarkable addition to the literature of the science of the mind."—The Los Angeles Times ). He has contributed to National Geographic, Slate, The New York Times, Gourmet, Harper's, The New Yorker, The American Scholar, and National Public Radio. Shenk's work inspired the Emmy-award winning PBS documentary The Forgetting and was featured in the Oscar-nominated feature Away From Her. His latest book, The Genius In All Of Us, was published in March 2010. Shenk has advised the President's Council on Bioethics
 Steven Ceci,S. J., On Intelligence: A bio-ecological treatise on intellectual development. 2nd ed., Harvard University Press. 1996. quoted in Shenk, Op. Cit.
 Richard E. Nisbett,Joshua Aronson and Clancy Blair, et al "Intelligence, New Findings and Theoretical Developments." American Psychologist, The American Psychological Association, vol. 66, no. 2 (February March 2012), 130-159, 130.
accessed 8/16/13. Nisbet is University of Michigan, Aronson and Blair are New York Univ.
other authors include, William Dickens ofNortheastern University, James Flynn University of Otago, Diane F. HalpernClaremont McKenna College,Eric Turkheimer
University of Virginia
 Tamra C. Daley,et al "IQ on the Rise, the Flynn effect Rural Kenyon Children." Psychological Science: A Journal of the Association for Psychological Science. vol. 14, no. 3, (May, 2003) 215-219.on line version http://pss.sagepub.com/content/14/3/215.short accessed 8/16/13
co authors include: Shannon E. Whaley2,Marian D. Sigman1,2,Michael P. Espinosa2 andCharlotte Neumann3
 Cosma Shalizi, "The Domestication of the Savage Mind," Book Rview of What is Intelligence, Beyond the Flynn Effect, by James Flynn, in American Scientist, Vol. 97, no. 3 (May-June, 2009) 244.
on line version: http://www.americanscientist.org/bookshelf/pub/the-domestication-of-the-savage-mind
Cosma Shalizi is an assistant professor in the statistics department at Carnegie Mellon University and an external professor at the Santa Fe Institute. He is writing a book on the statistical analysis of complex systems models. His blog, Three-Toed Sloth, can be found at http://bactra.org/weblog/.
 Angela Duckwork in the Proceedings of the National Academy of Sciences, quoted by Balter op.cit.
 New York Times book review, The Black and White Test score Gap, edited by Christopher Jenks and Meredith Philips. Washington DC: Bookings Institution Press. 1998. New York Times online
 Jeanna Bryner,"Men Smarter than Women Scientists Claim," Live Science, sept 8, 2006. On line resource or blog: http://www.livescience.com/7154-men-smarter-women-scientist-claims.html
 Metacrock, "Rejection of Christainty and Self Esteem," Review of a Study by Leslie J. Francis, et al." Atheist Watch, blog Oct, 25, 2010. http://atheistwatch.blogspot.com/2010/10/rejection-of-christianity-and-self.html accessed 8/15/13.
 Leslie J. Francis, in Research in the Social Scientific Study of Religion, Leiden, Netherlands: Koninklijke Brill NV, Ralph L. Piedmont, ed.,Volume 16, 2005, 2006, 108.
 Benson, P., & Spilka, B. (1973). quoted by Leslie J. Francis, in Ralph L. Piedmont, op.cit.
Francis attributes the quote to pages 209-210. Benson and Spilka study original source is:
God image as a function of self-esteem and locus of control.,Journal for the Scientific Study of Religion,
God image as a function of self-esteem and locus of control.,Journal for the Scientific Study of Religion,