实际上，穆斯林和基督教团体的宗教领袖可能认为，向教徒或信众提出反问，有利于社会和文化的教化事业。此外，他们还可以通过对这一领域开展研究，减轻新无神论错误信息对历史叙述的侵蚀影响。这类反问的一个例子是：新无神论的话语本身是否在阻碍科学发展。另一个例子是“第三种进化论”（Third Way of Evolution）团体，该团体拥有数百种科学观点，提出了一些非主流的进化思想，这些思想动摇了现代新达尔文主义综合理论（参见“第三种进化论”官方网站）。该网站的立论依据指出，新达尔文主义认为：

Realistically, religious leaders from Muslim and Christian communities may find it advantageous for the cause of social and cultural edification to propose counter-questions to congregation members or religious followers. Moreover, they may limit the corrosive impacts of New Atheist misinformation on historical narratives by conducting research into this area. Such a counter question is exemplified by asking whether New Atheist discourse is itself inhibiting to science. Another example is the Third Way of Evolution group which has hundreds of sciences consisting of non-normative evolutionary ideas which undermine the modern Neo-Darwinian synthesis (see Third Way of Evolution Website). On the website rationale, it states that neo Darwinism:

这一理论显然属于自然主义科学，但它忽视了许多当代分子证据，并依赖于一系列关于遗传变异偶然性质的无依据假设。新达尔文主义忽略了一些重要的快速进化过程，例如共生发生、水平基因转移、可移动DNA的作用以及表观遗传修饰。此外，一些新达尔文主义者把自然选择提升为唯一的创造力量，声称它能解决所有困难的进化问题，但这缺乏真正的经验依据（《进化的第三条道路》，2016年）。

Is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. NeoDarwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some NeoDarwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis (The Third Way of Evolution, 2016).

事实上，该组织的联合创始人之一丹尼斯·诺布尔博士（Dr. Denis Noble）不同意道金斯关于“自私的基因”的观点，但不愿就此问题与道金斯争辩（Crace, 2008）。某些“第三条道路”的科学成员可能被解读为完全拒绝达尔文式的进化机制。尤金·库宁（Eugene Koonin）提出的“生物大爆炸”就是例证，他认为“主要的新形态类型是通过从前一代重组实体的池中进行抽样过程而独立出现的”（Koonin, 2007, p.1）。据此，大卫·伯林斯基（Dr. David Berlinsky）在其针对道金斯的论战性著作中写道：“生物进化中的主要转变，”库宁写道：

Indeed, one of the organisation’s co-founders, Dr. Denis Noble, disagrees with Dawkins on the Selfish Gene idea but is reluctant to dispute Dawkins on the issue (Crace, 2008). Certain Third Way scientific members may be interpreted as rejecting the Darwinian evolutionary mechanism altogether. This is observed with Eugene Koonin’s proposal of a ‘biological Big Bang’ that supposes ‘the major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation’ (Koonin, 2007, p.1). From this Dr. David Berlinsky in his polemical work against Dawkins states, ‘Major transitions in biological evolution,’ Koonin writes:

这些正是达尔文理论本应加以解释的过渡。如果这些“重大过渡”代表的是新形态的“突然出现”，那么显而易见的结论不是自然界反常，而是达尔文错了（Berlinksy, 2009:192）。

These are precisely the transitions that Darwin’s theory was intended to explain. If those “major transitions” represent a “sudden emergence of new forms,” the obvious conclusion to draw is not that nature is perverse but that Darwin was wrong (Berlinksy, 2009:192).

一大批使用方法论自然主义表述观点的生物学家和其他专家，对达尔文理论的某些方面持有异议，但这一点被咄咄逼人的教条式新无神论者（如丹尼尔·丹尼特）轻描淡写地带过。丹尼特提出，达尔文的理论“毫无合理的怀疑余地”（Dennett, 1995, p.11）。从理论上讲，科学建立在归纳法之上，因此永远不可能是不可更改的，丹尼特在其他语境中也承认了这一点，他写道：“请注意，设计论证依赖于一个归纳推理：有烟的地方就有火；有设计的地方就有心智”（Dennett, 1995, p.30）。丹尼特若将“设计论证”一词替换为“整个达尔文式的事业”，便会有效地反驳他自己先前的主张。科学教条可以被定义为比宗教更能阻碍科学进步的东西，因为其中不存在“重叠的权威领域”（overlapping magisteria）的问题。

A wide array of biologists – who communicate methodologically naturalistic articulations - and other specialists disagree with aspects of Darwinian theory, but this is glossed over by dogmatic New Atheists like Daniel Dennett who proposes that Darwin’s theory is ‘beyond all reasonable doubt’ (Dennett, 1995, p.11). Theoretically, science is based on induction and can, therefore, never be incorrigible as indicated by Dennett in other contexts, stating ‘Note that the Argument from Design depends on an inductive inference: where there's smoke, there's fire; and where there's design, there's mind’ (Dennett, 1995, p.30). Dennett may substitute the words ‘arguments from design’ to ‘the entire Darwinian enterprise’ and effectively refute his own previous postulation. Scientific dogma may be defined as more inhibiting to scientific advancement than religion as there is no question of overlapping magisteria.