These questions remind me of an exchange from My Cousin Vinny (1992):
As a Catholic, I believe the Nicene Creed, which says in part: "I believe in one God, the Father almighty, maker of heaven and earth, of all things visible and invisible" (New Roman Missal). Thus, we believe by faith the reason why we exist, namely, God's creation of us, but we also have the ability through God-given reason to deduce how H. sapiens came to be. The overwhelming body of scientific evidence suggests not only an Earth that is billions of years old, but also that modern life has descended from previous life (the fact of evolution) and all life traces to a common ancestor.
Although the Bible is divinely inspired, I believe that although there are portions of the Bible that are written to be taken literally (like, for example, Jesus's command that we eat his flesh and drink his blood, or else we will have no life [Jn 6:53]), Genesis was not written as a scientific treatise (after all, the audience for whom it was written, who predates modern science by about 3000 years, would never be able to understand the modern scientific explanation for how people came to be) and is therefore not meant to be taken literally. Taking Genesis literally additionally leaves one with the uncomfortable position of having God (who is The Truth) create reason for us only to have us not use it with regards to an important question: our creation.
- How did life originate? How did life with hundreds of proteins originate just by chemistry without intelligent design?
- Properly speaking (and regardless of the opinions of some scientists), what we commonly understand to be the theory of evolution concerns itself with how life changed once the first life forms came into existence. Abiogenesis is separate and distinct from evolution.
- Nevertheless, the development of the first replicating molecules could have occurred during the early part of Earth's existence. It may be true that the odds are astronomically against life coming into existence naturally, but we should note that we are examining the question of how life began from the perspective of an Earth where life does exist. To borrow an analogy from John Allen Paulos's Innumeracy, one does not compute the astronomical odds against a particular board of bridge hands being dealt at random, look at a bridge board, and therefore conclude that the board was not randomly dealt. Likewise, the odds of winning the Powerball jackpot are incredibly long, yet, when someone does win, it would be silly to go back and conclude that the long odds meant that the drawing was fixed.
- How did the DNA code originate? The code is a sophisticated language system with letters and words where the meaning of the words is unrelated to the chemical properties of the letters—just as the information on this page is not a product of the chemical properties of the ink (or pixels on a screen). What other coding system has existed without intelligent design?
- First of all, the statement "The code is a sophisticated language system with letters and words where the meaning of the words is unrelated to the chemical properties of the letters" demonstrates a misunderstanding of protein structure and chemistry and how proteins are formed. Nucleic acids are transcribed to mRNA, and triplets of nucleotides are converted to amino acids through tRNA in translation. The sequence of amino acids determines the shape of the protein, which also affects its function, much as in mathematics, the sequence of digits in a number determines its value, which affects number theoretic properties (such as being prime). It is true, though, that the function of a protein cannot be trivially determined from its amino acid sequence, just as whether a number is prime cannot be trivially determined from its sequence of digits in the general case.
- I find a contract bridge analogy helpful. In contract bridge, there is an auction phase where the two partnerships compete to determine what the trump suit will be (or whether there will be a trump suit) and how many tricks a side wants to bid to take. During the auction, partners use the legal calls (bids, pass, double, redouble) to communicate the contents of their hands so that the optimal trump suit and number of tricks can be chosen. After modern contract bridge was created in 1925, various natural bidding systems arose. Bridge competitions pit systems against each other, and, in competitive play, the systems that produce the best results proliferate. This explains why some old techniques are almost unused at tournament play these days (notably strong two-bids being replaced by the artificial forcing 2 clubs opening for strong hands). Granted, bridge systems are filled with human inventions (such as the Stayman and Blackwood conventions). Nevertheless, competition has refined bridge bidding systems to best communicate the necessary information to reach the right contract, just as some scientists believe that evolution selected the universal RNA code to best communicate how to make the necessary proteins for life. In fact, the existence of a single universal RNA code in all organisms is strong evidence of common descent.
- How could such errors (mutations) create 3 billion letters of DNA information to change a microbe into a microbiologist? How can scrambling existing DNA information create a new biochemical pathway or nano-machines?
- This question mischaracterizes evolution, as evolution consists of not just mutations but also selection and heredity. To go back to the bridge example, one can be amazed by the sorts of systems that are in use today (see, for example, ), yet, through more than 85 years of play, we have seen systems and conventions (which, incidentally, use the same vocabulary of bridge bidding yet change or scramble the meaning of the of the bids) develop and gain popularity due to their ability to better communicate information and earn their users higher scores.
- The explanation to the question also asks how "32-component rotary motor like ATP synthase (which produces the energy currency, ATP, for all life), or robots like kinesin (a ‘postman’ delivering parcels inside cells) originate." It is well-understood how existing mechanisms can be adapted for new purposes, or how two different mechanisms can combine to form a new mechanism with a different function than either component. See  for ATP synthase and  for kinesin.
- Why is natural selection taught as ‘evolution’ as if it explains the origin of the diversity of life?
- Natural selection is not evolution, just as the infield fly rule is not baseball. Natural selection is a key mechanism of the theory of evolution. Other important mechanisms include artificial selection by humans (which is said to explain why carrots are orange ), mutations (how new DNA patterns originate, the "arrival of the fittest" mentioned in the explanation of the question) and heredity (how offspring inherit genetic material from their parent or parents).
- Also, the author of the questions does not provide any evidence that a reputable textbook or course teaches that natural selection is evolution.
- How did new biochemical pathways, which involve multiple enzymes working together in sequence, originate?
- As alluded to above, existing molecules and structures, through exaptation, can serve new functions, and, when put together, the combined pathway may serve an entirely different function than any constituent part.
- Living things look like they were designed, so how do evolutionists know that they were not designed? Why should science be restricted to naturalistic causes rather than logical causes?
- If a misguided physics student were to ask, "Kerry Wood's curveballs look like they are intelligently guided out of the strike zone, so how do physicists know that they were not intelligently guided?" as an attempt to refute dynamics, they would be understandably ridiculed, because the question is loaded and ridiculous. God certainly may have guided Wood's curveballs out of the strike zone, but this does not negate the laws of physics that explain very well why curveballs curve out of the strike zone. Likewise, life may certainly have been created by an intelligent being, but this does not negate the principles of the theory of evolution that explain very well the diversity of life and how it changed over time from the first life to the present.
- Just as law has ground rules for the admission of evidence that a judge or jury can consider, science has ground rules for the admission of explanations of natural phenomena. A key principle of science is that any explanation ought to be possible to falsify based on experiments using the five human senses. Admitting supernatural explanations, even if they happen to be true, contradicts this key part of science and the scientific method.
- How did multi-cellular life originate?
- Unicellular organisms can band together for mutual support and protection. Those organisms can engage in sacrificial behavior that is for the good of the entire group. Then, this relationship can change into a relationship where cells band together as part of an multicellular organism.
- In fact, during the research of my response to this question, I discovered an article in PNAS describing an experiment in which unicellular yeasts from species Saccharomyces cerevisiae were subject to an experiment that selected on the basis of gravity, with the experimenter selecting the organisms falling to the bottom of a liquid tube. Within 60 days, the experimenter saw the development of true multicellular yeasts.
- How did sex originate?
- Why are the (expected) countless millions of transitional fossils missing?
- How do ‘living fossils’ remain unchanged over supposed hundreds of millions of years?
- First, the quote by Dr. Gould in the author's explanation of this question is taken out of context. Gould wrote:
|“||Although punctuated equilibrium deals directly only with stability of species through time, the higher-level analogue of non-trending in larger clades has also graduated from an undefined non-subject to a phenomenon worth documenting. Moreover, because spcies often maintain stability through such intense climatic change as glacial cycling, stasis must be viewed as an active phenomenon, not a passive response to unaltered environments. Many leading evolutionary theorists, while not accepting our preference for viewing stasis in the context of habitat tracking or developmental constraint, have been persuaded by punctuated equilibrium that maintenance of stability within species must be considered as a major evolutionary problem||”|
—S. J. Gould, Nature 366:223-224 (18 Nov. 1993)
- It is undisputed that there are unique populations that have not changed for millions of years. One evolutionary explanation would be that without the pressures of natural selection within a habitat, evolution would not function to change those populations. However, as Gould points out, this explanation is inadequate. Gould's argument is that how evolution operates is through punctuated equilibrium, which is to say that most populations do not change for a long time and then change rapidly over short periods of time. Note that this is different from Darwin's vision of how populations change over time (his one diagram in On the Origin of Species describes the view of gradualism).
- How did blind chemistry create mind/intelligence, meaning, altruism and morality?
- Evolution is not blind chemistry. It is easy to see how altruism and morality can lead to differential reproductive success on which natural selection can operate. For example, chickens have a pecking order that determines which members of a population get the first chance at food. The members of the population could compete every time there is food, but this would waste energy (possibly more than is contained in the food). Likewise, we humans should be glad that we do not have to fight to get to the cashier in a restaurant, for we have developed queueing. It is also easy to see how altruism develops in a population, since altruism can increase the reproductive success of a population. Any biology student could explain how mutations increasing intelligence are selected for in evolution: in many cases (but not all), greater intellectual capacity can increase reproductive fitness.
- With regards to meaning, the author of the 15 questions suggests that evolutionists believe that "we invented God." This is not true. Some scientists who believe in evolution suggest that creation of myths of supernatural beings in the human mind may improve reproductive fitness by entrenching the moral/altruistic behaviors that we have already seen provide additional reproductive success. As a Catholic, I happen to disagree with them, of course. Meaning is essentially a philosophical question, and not within the ambit of science or the theory of evolution. Some scientists may have a view on these matters (Dr. Miller and Dr. Dawkins will naturally disagree), but not every statement made by a scientist is a scientific statement.
- Why is evolutionary ‘just-so’ story-telling tolerated?
- First of all, it is ironic that this charge is being levied by an author affiliated with a group that believes a literal interpretation of Genesis (including creation having occurred during six 24-hour periods) explains everything there is to know about the origin and diversity of life. See, for example, . From a scientific point of view, it is hard to see this belief as anything other than a "just-so" story.
- In any case, evolution is not a just-so story. One, there is overwhelming evidence supporting not only the fact that evolution has occurred but also the theory that explains why changes in populations over time have occurred. Two, scientists have legitimate disagreements over exactly how evolution works. For example, Gould believes that changes to populations occur in rapid bursts separated by long periods of stasis (punctuated equilibrium); others disagree. Likewise, some scientists believe that H. sapiens developed in Africa as a separate species, spread through the other continents, and displaced H. erectus by competition, while others contend that the global H. erectus population split geographically and independently developed into H. sapiens. If evolution were a "just-so" story, we would not have biologists conducting evolutionary research. But we do see new and exciting discoveries in evolutionary biology, which indicates not only that evolution is not a "just-so" story but in fact has unresolved issues to which eager researchers want to find explanations.
- Where are the scientific breakthroughs due to evolution? Why do schools and universities teach evolution so dogmatically, stealing time from experimental biology that so benefits humankind?
- Why is evolution, a theory about history, taught as if it is the same as this operational science?
- Why is a fundamentally religious idea, a dogmatic belief system that fails to explain the evidence, taught in science classes? If “you can’t teach religion in science classes”, why is evolution taught?
- If the protein is folded correctly, see http://en.wikipedia.org/wiki/Protein_folding