Daniel McShae and Michael Brandon, Biology's First Law :The Tendency for Diversity and Complexity to Increase in Evolutionary Systems, 2010
The history of life presents three great sources of wonder. One is adaptation, the marvelous fit between organism and environment. The other two are diversity and complexity, the huge variety of living forms today and the enormous complexity of their internal structure. Natural selection explains adaptation. But what explains diversity and complexity? (location 78)

Based on what we have said so far, some will be poised and ready to make a leap, from the notion of accumulation of accidents to the second law of thermodynamics…. We advise readers against this, for their own safety. We are concerned that on the other side of that leap there may be no firm footing. Indeed, there may be an abyss. First, we think the foundation of the ZFEL [zero-force evolutionary law] lies in probability theory, not in the second law or any other law of physics. And second, our notions of diversity and complexity differ fundamentally from entropy, in that entropy, unlike diversity and complexity is not a level-related concept. (location 220)

Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, 2009
By the time Darwin came to publish On the Origin of Species in 1859, he had amassed enough evidence to propel evolution itself, though still not natural selection, a long way towards the status of fact. Indeed, it was this elevation from hypothesis towards fact that occupied Darwin for most of his great book. The elevation has continued until, today, there is no longer any doubt in any serious mind, and scientists speak, at least informally, of the fact of evolution. All reputable biologists go on to agree that natural selection is one of its most important driving forces, although —as some biologists insist more than others—not the only one. Even if it is not the only one, I have yet to meet a serious biologist who can point to an alternative to natural selection as a driving force of adaptive evolution—evolution towards positive improvement. (p. 18)

When creationists say, as they frequently do, that the theory of evolution contradicts the Second Law of Thermodynamics, they are telling us no more than that they don’t understand the Second Law (we already knew that they don’t understand evolution). There is no contraction, because of the sun!…energy from the sun powers life, to coax and stretch the laws of physics and chemistry to evolve prodigious feats of complexity, diversity, beauty, and an uncanny illusion of statistical improbability and deliberate design…Natural selection is an improbability pump: a process that generates the statistically improbable. It systematically seizes the minority of random changes that have what it takes to survive, and accumulates them, step by tiny step over unimaginable timescales, until evolution eventually climbs mountains of improbability and diversity, peaks whose height and range seem to know no limit, the metaphorical mountain that I have called ‘Mount Improbable’…Life evolves greater complexity only because natural selection drives it locally away from the statistically probable towards the improbable. (p. 415)

Marc Kirschner and John Gerhart, The Plausibility of Life: Resolving Darwin’s Dilemma, 2005
Facilitated variation is not like orthogenesis, a theory championed by the eccentric American paleontologist Henry Osborn (1857–1935), which imbues the organism with an internal preset course of evolution, a program of variations unfolding over time. Natural selection remains a major part of the explanation of how organisms have evolved characters so well adapted to the environment. (page 247)

By comparison, if we question how long it would take a high-speed computer to write randomly a specific Shakespearean sonnet, we are asking that all the letters of the words of the sonnet will come up simultaneously in the correct order. It is an impossible task, even if all the computers in the world today had been working from the time of the big bang to the present. Even to compose the phrase, “To be or not to be,” letter by letter, would take a typical computer millions of years. (page 32)

Charles Darwin, The Origin of Species
To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.

al-Jāḥiẓ, The Book of Animals, 9th century
Animals engage in a struggle for existence [and] for resources, to avoid being eaten and to breed....Environmental factors influence organisms to develop new characteristics to ensure survival, thus transforming into new species. Animals that survive to breed can pass on their successful characteristics to [their] offspring.

Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism, 2007
P. falciparum, HIV, and E. coli are all very, very different from each other. They range from the simple to the complex, have very different life cycles, and represent three different fundamental domains of life: eukaryote, virus, and prokaryote. Yet they all tell the same tale of Darwinian evolution. Single simple changes to old cellular machinery that can help in dire circumstances are easy to come by. This is where Darwin rules, in the land of antibiotic resistance and single tiny steps…There is no evidence the Darwinian process can take the multiple, coherent steps needed to build new molecular machinery, the kind of machinery that fills the cell. (page 162)

Kenneth Miller, Only a Theory: Evolution and the Battle for the American Soul, 2008
In Behe’s view, these are examples of nothing more than a kind of “trench warfare” in which the two species have progressively disabled or broken parts of themselves in order to survive. Nothing genuinely new, novel, or complex has resulted from this struggle, and we shouldn’t expect otherwise. The reason, according to Behe, is that the sorts of changes we see in this well-studied interaction represent the limit, the “edge” of what evolution can accomplish. They can go this far and no further. A line in the sand is drawn, and the other side of that line is intelligent design.  How does Behe know where to draw that line? (page 67)

It would be an act of unbridled arrogance for us to examine the living history of this planet and pronounce ourselves, in Gould’s words, “the summit of life’s purpose.” Run the tape of life again, starting from the Cambrian or wherever one might choose, and it’s almost inconceivable that you’d get hairless bipedal primates with brains big enough to endow them with self-awareness, reflective thought, and calculus. (p. 152)

Christine Kenneally, The First Word: The Search for the Origins of Language, 2007
They [Pinker and Bloom] particularly emphasized that language is incredibly complex, as Chomsky had been saying for decades. Indeed, it was the enormous complexity of language that made is hard to imagine not merely how it had evolved but that it had evolved at all…..But, continued Pinker and Bloom, complexity is not a problem for evolution. Consider the eye. The little organ is composed of many specialized parts, each delicately calibrated to perform its role in conjunction with the others. It includes the cornea,…Even Darwin said that it was hard to imagine how the eye could have evolved…….And yet, he explained, it did evolve, and the only possible way is through natural selection—the inestimable back-and-forth of random genetic mutation with small effects…Over the eons, those small changes accreted and eventually resulted in the eye as we know it. (page 59)

Stephen M. Barr, quoted in "The Mythological Conflict Between Christianity and Science | An interview with physicist Dr. Stephen Barr," Ignatius Insight, September 25, 2006
But are they right [advocates of ID] in saying that the Darwinian mechanism is inadequate to explain biological complexity? Most biologists, including most of those who are devout Christian believers, doubt it very strongly. And even if the ID people are right, it will be virtually impossible to prove that they are right because they are asserting a negative. They are saying that no Darwinian explanation of certain complex structures will ever be forthcoming. Well, there may not exist such an explanation now, but there might exist one later. So, in practice, I don't see a slam-dunk proof for miraculous intervention in evolution as coming out of this movement.

Stephen M. Barr, Modern Physics and Ancient Faith, 2003
However, having started with the empirically quite unsupported postulate of atheism, the materialists is practically forced to call a variety of empirical facts “illusions”—not facts that are in front of his eyes, but are behind his eyes, so to speak, facts about his own mind….None of this is to deny that there are some very hard questions that arise from the idea that the human mind is not entirely reducible to matter. There certainly are. For instance, if there is something immaterial about the mind, how does it affect the brain and body? (location 4612)

Niel Campbell and Jane Reece, Biology
Each of the four identical polypeptide chains that together make up transthyretin is composed of 127 amino acids…The primary structure is like the order of letters in a very long word. If left to chance, there would be 20 to the 127th power different ways of making a polypeptide chain 127 amino acids long. (page 82, 7th edition)

And certain properties of the human brain distinguish our species from all other animals. The human brain is, after all, the only known collection of matter that tries to understand itself. To most biologists, the brain and the mind are one and the same; understand how the brain is organized and how it works, and we’ll understand such mindful functions as abstract thought and feelings. Some philosophers are less comfortable with this mechanistic view of mind, finding Descartes’ concept of a mind-body duality more attractive. (4th edition, p.776)

"Natural Selection and the Complexity of the Gene: Conflict between the idea of natural selection and the idea of uniqueness of the gene does not seem to be near a solution yet," Nature
Modern biology is faced with two ideas which seem to me to be quite incompatible with each other. One is the concept of evolution by natural selection of adaptive genes that are originally produced by random mutations. The other is the concept of the gene as part of a molecule of DNA, each gene being unique in the order of arrangement of its nucleotides. If life really depends on each gene being as unique as it appears to be, then it is too unique to come into being by chance mutations. There will be nothing for natural selection to act upon. (Vol. 224, 1969, page 342)

Ludwig von Bertalanffy, “Chance or Law,” in Beyond Reductionism: New Perspectives in the Life Sciences, 1969
Considered thermodynamically, the problem of neo-Darwinism is the production of order by random events. (page 76)

"Thermodynamics of evolution: The functional order maintained within living systems seems to defy the Second Law; non-equilibrium thermodynamics describes how such systems come to terms with entropy," Physics Today 25(11), 23 (1972)**
Unfortunately this principle cannot explain the formation of biological structures. The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred….The conclusion to be drawn from this analysis is that the apparent contradiction between biological order and the laws of physics—in particular the second law of thermodynamics—cannot be resolved as long as we try to understand living systems by the methods of the familiar equilibrium statistical mechanics and equally familiar thermodynamics.

Karen Horney, The Neurotic Personality of Our Time, New York: Norton, 1937
Let us consider for example, a person listening to a paper and having critical thoughts about it. A minor inhibition would consist in a timidity about expressing the criticism; a strong inhibition would prevent him from organizing his thoughts, with the result that they would occur to him only after the discussion was over, or the next morning. But the inhibition may go so far as not to permit the critical thoughts to come up at all, and in this case, assuming that he really feels critical, he will be inclined to accept blindly what has been said or even to admire it; and he will be quite unaware of having any inhibitions. In other words, if an inhibition goes so far as to check wished or impulses there can be no awareness of its existence.(page 55)

Thomas Nagel, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False, 2012
Among the traditional candidates for comprehensive understanding of the relation of mind to the physical world, I believe the weight of evidence favors some from of neutral monism over the traditional alternatives of materialism, idealism, and dualism. (location 69)

Jean-Paul Sartre, Being and Nothingness: A Phenomenological Essay on Ontology, New York: Washington Square Press
Thus the passion of man is the reverse of that of Christ, for man loses himself as man in order that God may be born. But the idea of God is contradictory and we lose ourselves in vain. Man is a useless passion. (page 784)

Mueller, Marvin, "The Shroud of Turin: A Critical Appraisal," The Skeptical Inquirer
There are only three classes of possibilities for the image formation: by human artifice, through natural processes transferring the image to the linen from a real crucified corpse, or by supernatural means. Of the third, not much can be said, because then all scientific discussion and all rational discourse must perforce cease.…But a lot can be said about natural processes. In terse summary, they can be ruled out definitely by the quality and beauty of the shroud image. (Spring 1982, page 27)

Robert Spitzer, New Proofs for the Existence of God: Contributions of Contemporary Physics and Philosophy, 2010
Acts of self-consciousness (awareness of awareness) are difficult to explain through regular space-time models (one act of awareness capturing itself, as it were). (location 2211)

Georgi P. Gladyshev, “Thermodynamic Theory of Biological Evolution and Aging. Experimental Confirmation for Theory”
On the whole, one may assert that both internal factors (characteristics of the biosystem) and external factors (characteristics of the environment) determine the trend of biological evolution, whose progress is, of course, possible thanks to the inflow of solar energy and energy from other sources. (Entropy 1999, 1(4), 55-68, www.mdpi.org/entropy/ doi:10.3390/e1040055)

Henry Morris, “Does Entropy Contradict Evolution?”
If science is to be based on fact and evidence, rather than metaphysical speculations, then entropy does not explain or support evolution at all. In fact, at least until someone can demonstrate some kind of naturalistic comprehensive biochemical predestinating code and a pre-existing array of energy storage-and-conversion mechanisms controlled by that code to generate increased organized complexity in nature, the entropy law seems to preclude evolution altogether. The marvelously complex universe is not left unexplained and enigmatically mysterious by this conclusion, however. It was created by the omnipotent and omniscient King of Creation! If evolutionists prefer not to believe this truth, they can make that choice, but all the real facts of science - especially the fundamental and universal law of entropy - support it. (http://www.icr.org/article/does-entropy-contradict-evolution/)

Richard Dawkins, The God Delusion, 2006
A dualist acknowledges a fundamental distinction between matter and mind. A monist, by contrast, believes that mind is a manifestation of matter—material in a brain or perhaps a computer—and cannot exist apart from matter. A dualist believes the mind is some kind of disembodied spirit that inhabits the body and therefore conceivably could leave the body and exist somewhere else. (p. 180)

Daniel Dennet, Breaking the Spell: Religion as a Natural Phenomena, 2006
In its scientific or philosophical sense, it [materialism] refers to a theory that aspires to explain all the phenomena without recourse to anything immaterial—like a Cartesian soul, or“ectoplasm”—or God. The standard negation of materialistic in the scientific sense is dualistic, which maintains that there are two entirely different kinds of substance, matter and…whatever minds are supposedly made of. (p. 302)

Stephen Jay Gould, Natural History, March 1997
Catholics could believe whatever science determined about the evolution of the human body, so long as they accepted that, at some time of his choosing, God had infused the soul into such a creature. I also knew that I had no problem with this statement, for whatever my private beliefs about souls, science cannot touch such a subject and therefore cannot be threatened by any theological position on such a legitimately and intrinsically religious issue. (13th paragraph)

Anthony Kenny, What I Believe, 2006
What is peculiar to our species is the capacity for thought and behavior of the complicated and symbolic kinds that constitute the linguistic, social, moral, economic, scientific, cultural and other characteristic activities of human beings in society. The mind is a capacity, not an activity: it is the capacity to acquire intellectual abilities of which the most important is the mastery of language. The will, in contrast with animal desire, is the capacity to pursue goals that only language-users can formulate. (p. 69)

If we reflect on the social and conventional nature of language, we find something odd in the idea that language may have evolved because of the advantages possessed by language users over non-language users. It seems as absurd as the idea that banks may have evolved because those born with an innate cheque-writing ability were better off than those born without it. (p. 25)

I do not share the extreme skepticism of many scholars, including Christian scholars, about the historical value of the Gospels. For instance, that Jesus at his last meal took bread and wine and said something like “this is my body, this is my blood” seems to me to be as likely to be true as anything that is narrated in the records of the early Roman Empire. With regard to the Acts of the Apostles, I have long been amused to note that Catholic biblical scholars often appear less ready to accept them as broadly historical than are atheists colleagues in ancient history departments. (p. 58)

Lee Silver, Challenging Nature: The Clash of Science and Spirituality, 2006
Free will is commonly interpreted to mean “the power of directing our own actions without [total] constraint by necessity or fate.” The conviction that human beings are endowed with such a power is pervasive, even more so than a belief in the human soul…As a philosophical concept, free will is like an onion whose skin has been completely peeled away: at its core, it ceases to exist. (p. 59)

Merlin Donald, A Mind So Rare, 2002
This book proposes a theory of consciousness that stays carefully on the functional level and does not to try to “explain” how awareness could have emerged from a material thing such as a brain. I believe that we might someday understand how this came to be. However, in my opinion, our present intellectual and scientific resources are not sufficient to give us even the beginnings of such a theory. (p. 9)

“Neuroscience vs philosophy: Taking aim at free will,” Published online 31 August 2011, Nature 477, 23-25 (2011)
There are conceptual issues — and then there is semantics. "What would really help is if scientists and philosophers could come to an agreement on what free will means," says Glannon. Even within philosophy, definitions of free will don't always match up. Some philosophers define it as the ability to make rational decisions in the absence of coercion. Some definitions place it in cosmic context: at the moment of decision, given everything that's happened in the past, it is possible to reach a different decision. Others stick to the idea that a non-physical 'soul' is directing decisions.

Charles Darwin, Descent of Man
If the various checks specified in the last two paragraphs, and perhaps others as yet unknown, do not prevent the reckless, the vicious and the otherwise inferior members of society from increasing at a quicker rate than the better class of men, the nation will retrograde, as has too often occurred in the history of the world. We must remember that progress is no invariable rule. (Amherst, NY: Prometheus Books, 1998, p. 145)

Herbert Spencer, Social Statics
It seems hard that an unskillfulness which with all his efforts he cannot overcome, should entail hunger upon the artizan. It seems hard that a labourer incapacitated by sickness from competing with his stronger fellows, should have to bear the resulting privations. It seems hard that widows and orphans should be left to struggle for life or death. Nevertheless, when regarded not separately, but in connection with the interests of universal humanity, these harsh fatalities are seen to be full of beneficence—the same beneficence which brings to early graves the children of diseased parents, and singles out the intemperate and the debilitated as the victims of an epidemic. [Social Statics, Abridged and Revised; Together with Man Versus the State, New York: D. Appleton & Company (1903), p. 150]

Ernst Haekel, quoted by Richard Weikart, From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in German, 2004
The difference between the highest and the lowest humans is greater than that between the lowest humans the highest animal.(page 10)

John Dewey, http://www.harvardsquarelibrary.org/philosophers/john_dewey.php
The idea that “God” represents a unification of ideal values that is essentially imaginative in origin when the imagination supervenes in conduct is attended with verbal difficulties owing to our frequent use of the word “imagination” to denote fantasy and doubtful reality. But the reality of ideal ends as ideals is vouched for by their undeniable power in action.These considerations may be applied to the idea of God, or, to avoid misleading conceptions, to the idea of the divine. The idea is, as I have said, one of ideal possibilities unified through imaginative realization and projection. But this idea of God, or of the divine, is also connected with all the natural forces and conditions—including human associations—that promote the growth of the ideal and that further its realization. We are in the presence neither of ideals completely embodied in existence nor yet of ideals that are mere rootless ideals, fantasies, utopias. For there are forces in nature and society that generate and support the ideals. They are further unified by the action that gives them coherence and solidarity. It is this active relation between ideal and actual to which I would give the name “God.” I would not insist that the name must be given.

Marcus Borg, Meeting Jesus Again for the First Time: The Historical Jesus & the Heart of Contemporary Faith, 2005
I was experiencing a collision between the modern worldview and my childhood beliefs. The modern worldview, with its image of what is real as the world of matter and energy and its vision of the universe as a closed system of cause and effect, made belief in God—a nonmaterial reality—increasingly problematic. I had entered the stage of critical thinking, and there was no way back.( p. 7)

Niccolò Machiavelli, The Prince
From this it may be concluded that men should either be caressed or exterminated, because they can avenge light injuries, but not severe ones. The damage done to a man should be such that there is no fear of vengeance. (The Prince and Other Works, Translation, Introduction and Notes by Allan H. Gilbert, New York: Hendricks House, 1964, p. 99)