Question Evolution

Question Evolution is a self-described "grass roots" campaign created by the young Earth creationist organization Creation Ministries International (CMI). It is being jointly promoted in the United States by the anti-gay hate group Traditional Values Coalition, which claims that it lobbies for over 43,000 churches in the USA.Active Anti-LGBT Groups Southern Poverty Law Center The campaign's stated objective is to encourage high-schoolers, college students, and non-scientists to question the validity of evolution and make up their own minds about the subject.Creation advocates start a campaign to ‘question evolution’, Conservative News and Views, 4 May 2011 Which, much like "teach the controversy", really means "deny the validity of evolution and think what CMI thinks".
The Question Evolution campaign is not genuinely concerned with posing difficult scientific questions. Rather, it is centered around the distribution of a religious tract called "15 Questions for Evolutionists",15 Questions for Evolutionists Creation Ministries International which purports to ask "15 critically important questions that evolutionists cannot adequately answer."Creation.com's Question Evolution page (Yes, they do have a poor grasp of English grammar.) The tract cannot be seriously described as a legitimate educational resource; instead, it is an obvious tool for the further indoctrination or reinforcement of uncritically-held dogmatic and anti-science beliefs.
In principle, questioning any scientific theory is a very good idea when the aim is to critically examine the evidence rather than cherry-pick evidence that confirms a faith-based position, as creationists largely do. Science is an evidence-based process of attempting to provide naturalistic explanations for natural events. In that light, legitimate scientists never stop asking questions, even when they already have a "good" theory. Many valid scientific questions remain about the theory of evolution and are asked and explored every day by scientists studying their field.
===CMI's 15 questions fall into several broad categories===
 
 Ones that are adequately answered by the theory of evolution, with its vast explanatory and predictive power; creationists reject these answers because they conflict with their religious dogma.
 Questions 5, 6, 8, 10, 13, 14
 
 
 Questions that flat-out misrepresent the state of the science.
 Questions 1, 7, 8, 11, 12 
 
 
 Some questions are derived from religious beliefs that have nothing to do with the scientific question of whether the theory of evolution adequately explains the diversity of life on Earth.
 Questions 1, 12
 
 
 Some rely on vague rather than scientific definitions, such as with "information", a term only creationists use in this context. Or straw man versions of such definitions and ideas, such as claiming the theory of evolution states we're all just an "accident" because of random chances.
 Questions 3, 4, 5, 11
 
 
 Ones that misrepresent the nature of the theory of evolution as "just-so story telling", a "fundamentally religious idea" and "dogmatic belief system", and a hindrance to scientific advancement, which, even if true, are contentless claims and irrelevant to whether the theory of evolution is good science. They thereby merely badmouth the theory's explanatory power rather than make any principled argument.
 Questions 4, 12
 
 
 Many questions are predicated on the false notion that no sound conclusions can be drawn about unobserved events in the past — this assertion is frequently trotted out to falsely elevate the standing of creationism to that of the theory of evolution by asserting that they're both equally unscientific.
 Questions 4, 12, 14, 15
 
 
 Several questions ask about irrelevant matters such as biogenesis and even morality. These questions are only interesting because they highlight the degree to which both sides of the discussion are talking past each other.
 Questions 1, 3, 4, 11
 
And finally, as in any area of scientific inquiry…
 
 ... many questions cannot presently be answered because of our limited knowledge. The modern evolutionary synthesis of Darwinian natural selection, Mendelian genetics, and population genetics is a recent scientific development that is highly dependent on technological innovations.It was only in the 1930s that Mendelian genetics was proposed as a mechanism of evolution, and 1952 that the Hershey-Chase experiment confirmed that DNA is the operative material of genetics. Significant advances in molecular biology run apace and even snowball, yet it is only creationists who are so demanding of the scientific community that it answer all these questions right this very moment. And even then, their focus is strictly on scientific fields perceived to conflict with their peculiar religious dogma; one will never see similar impatience directed toward "creation scientists'" failure to advance their various "fields of study". Nor will creationists ever be critical of the 218 intervening years between Isaac Newton's 1687 Principia and Albert Einstein's 1905 On the Electrodynamics of Moving Bodies.
 Questions 1, 2, 5, 7, 8, 9, 11
 
Obviously — and fortunately for those studying the science of evolution — there are a vast number of open questions in the last category, all of which are under active consideration. CMI, however, would like people to draw the conclusion that any unanswered question means:
 
 It will never be answered (or has been answered with Ultimate Authority). ...
 ... because God did it.
CMI could have read the literature and come up with a series of interesting and challenging questions based on what evolutionary scientists are presently investigating — although that would have involved some honest research and understanding of the subject. But instead of concentrating on these real questions, CMI employs the typical creationist strategy of dissembly and deflection by perpetuating myths and misconceptions about the theory of evolution, all while making money selling religious tracts, t-shirts, buttons, hats, bumper stickers, coffee cups, and tote bags.Products meeting the search criteria Creation Ministries USAhttp://www.cafepress.com/creationstuff
==15 Questions for Evolutionists==
Without further ado:
===1. How did life originate?===
This first question is actually entirely irrelevant — evolution does not claim to explain the origin of life, nor has it ever attempted to do so. CMI is here implying that the theory of evolution is false because it does not offer a complete explanation of abiogenesis (the technical term for "the Origin of Life"). However, this does not logically follow. It would be like faulting chemistry for not explaining where matter comes from.
Biological evolution simply refers to "descent with modification", or the change of allele frequencies among a discrete population of organisms over time. Evolution occurs when genetic mutations have either a positive or negative impact on the organism's fitness to survive in its environment leading to (usually subtle and usually imperceptible) changes in its morphology. When compiled over successive generations, cumulative genotypic changes manifest significant enough phenotypic differences between discrete populations of organisms that they can no longer interbreed, leading to speciation. This and similar explanations of biodiversity, such as genetic drift, are evolution's sole concerns, not the origin of life itself.
====Science and abiogenesis====
The question of how life originated is presently unanswered because science is not sufficiently advanced in that field, and the quote by Paul Davies used by CMI is perfectly truthful. However, the lack of an explanation for abiogenesis has nothing to do with the truth or falsity of the theory of evolution. 
CMI seems to be trying to imply that evolution cannot be valid while a related field of study has unresolved issues. This is demonstrably false, as it would not be the first time when one scientific field has advanced while a related field was stalled. From the 1750s until the early 1900s, enormous advances were made in the field of chemistry, despite there being no verified explanation as to why any of it actually worked. The underlying mechanics of chemistry were not identified until the development of atomic physics in the early 20th century. It may well be quite some time before we achieve any scientific consensus on the mechanics of abiogenesis, but this has no bearing on the fact that life clearly exists, and it changes in accordance with the theory of evolution.
Regardless, abiogenesis is certainly an active area of research. One aspect it has clearly established is that "life" itself is an ambiguous term. There is a continuum between non-life and life, and organisms such as viruses or prions occupy a place on that continuum that is difficult to define. 
Current research paths for abiogenesis are focusing on autocatalytic and self-assembling nucleobases (usually into RNA) that can easily emerge spontaneously in the lab.James P. Ferris, et. al, "Synthesis of long prebiotic oligomers on mineral surfaces", Nature, Vol. 381, 2 May 1996, pp. 59-61 The building blocks upon which RNA and DNA operate to create peptides (polymers of amino acids) can also spontaneously emerge in the lab. Miller and Urey's famous 1953 paper discussed the spontaneous creation of 5 amino acids in a sealed flask under hypothesized conditions on the early Earth. Shortly after the paper was published, further analysis proved the presence of carboxylic and hydroxy acids, which are used biologically for long-chain polymerization. The flask upon which they based the paper was analyzed using contemporary methods and determined to contain not just the initial 5 amino acids but 14 amino acids and 5 amines, which include the byproducts of amino acid breakdown and signaling chemicals used for intercellular communication. Still, later analysis of a flask that Miller and Urey did not analyze for their paper revealed the presence of 22 amino acids and 5 amines.Indiana University. "'Lost' Miller-Urey Experiment Created More Of Life's Building Blocks." ScienceDaily, 17 Oct. 2008. Web. 6 Jul. 2011. This exciting research confirms without a doubt that complex and autocatalyzing and self-assembling chemicals and the chemicals upon which they operate can form spontaneously in the lab.
====Proteins self-assembling====
The commentary on the question provided by CMI states "Even if every atom in the universe were an experiment with all the correct amino acids present for every possible molecular vibration in the supposed evolutionary age of the universe, not even one average-sized functional protein would form."
This may seem plausible at first glance, but it is an entirely unsubstantiated assertion and one that is almost entirely contradicted by the available evidence. 
Self-assembly is an intrinsic aspect of chemistry; otherwise, there would be no molecules of any kind. All molecules seek the lowest energy state,Refer to any discussion of thermodynamics and entropy if this seems unclear. and if combining yields a lower energy state than being separate, two atoms or molecules will combine spontaneously. Even when this is not the case, in the presence of external energy sources and catalysts, atoms and molecules may still combine, as long as the overall energy state (i.e. the total energy state of the sources and recipients combined) ends up lower. All of the organic molecules (amino acids, phosphates, lipids, etc.) present in a cell have been demonstrated to spontaneously assemble, given the right conditions. Some have been discovered on meteors, indicating they can form in space. Even complex protein precursors such as polypeptides (strings of amino acids) have been demonstrated to spontaneously assemble in the right conditions.
So this is not a discussion of whether random atoms can combine to form a protein. This is a discussion of whether or not polypeptides (already demonstrated to spontaneously assemble from amino acids, which have been demonstrated to spontaneously assemble from molecules, which spontaneously assemble from individual atoms) can randomly assemble to form a protein. And while the answer is currently "no, this has not been demonstrated", it is nowhere near as unlikely as CMI is attempting to suggest. As current belief is that life emerged around 500 million years after the Earth was formed, this seems like plenty of time for a protein to spontaneously form.
So the claim is, even assuming the "supposed evolutionary age of the universe" (i.e. 13.8 billion years),"Evolutionary age" is a creationist code word for "older than 6,000 years and therefore incompatible with our dogmatic worldview." functional proteins emerging from a primordial soup is so improbable that the only acceptable explanation is to assume a designer (goddidit). This is fundamentally an argument from ignorance premised on CMI's refusal or inability to honestly consider the evidence and likely explanations. It is also predicated on the logically unsound premise that highly improbable events do not occur, which is known to be false. Just because the odds of something occurring are too small for a creationist (read: idiot) to conceive of, they are not therefore zero. Improbable things happen all the time. People get struck by lightning. Someone will eventually win the lottery. Proteins are highly likely to form, given enough time.
Finally, CMI picked the wrong target in choosing a protein as their case in point. A better target would have been a prokaryote (single-celled organisms without a nucleus, such as bacteria), as this requires not only proteins but the machinery to replicate them. However, the same argument used for the evolution of a protein applies here — there are scientifically verified forces of self-organization at work, so it is not a truly "random" process as they are claiming. There is a huge amount of research being done on these early proto-life structures with some fascinating potential benefits (such as random chemistry being used to produce new drugs and vaccines). CMI's thought process of trying to calculate the odds of a prokaryotic-like organism spontaneously arising is a perfect example of how embracing creationist dogma would kill scientific progress and knowledge.Which, given that they seem to see science as a grave threat to their faith, may be exactly what they want.
====CMI's motive behind the question====
This question was likely chosen as the first because it is undoubtedly the strongest argument against scientific thought that the Creationists have — science openly admits it does not have an acceptable answer to this question. The fact that it is irrelevant to the stated intent to "Question Evolution" does not seem to matter; the objective here is to build distrust of science, on the principle that people will then assume that if science's answer isn't quite right, the right answer must be a specific interpretation of one specific religion's creation story.
The problem creationists have with evolution is not that it challenges belief in God, because it doesn't. Their problem is that evolution (like many other fields of science, such as geology, astronomy, and physics) challenges the accuracy and authority of a literal interpretation of the Bible. Genesis makes some concrete claims about the abundance of life on this planet (both in terms of the creation story and of the Global Flood). As such, creationists believe that if evolution is true, their literal reading of Genesis is not, and since their literalist dogma asserts that said literal reading of Genesis is correct, they assume that anything else must be false. What is not correct is the belief that the theory of evolution necessarily supplants any need for a belief in a god. A lot of theists accept the theory of evolution and still maintain devoted religious lives. They're just not biblical literalists.
In any event, CMI gets abiogenesis wrong. The most fundamental mistake CMI makes is to define life based on what we observe in the complex organisms we see today. The group then tries to calculate the odds of this form of life arriving spontaneously. This is a classic "argument from incredulity". Early life would look vastly simpler than what we see today and likely did not involve protein synthesis at all. Do scientists know what this life actually looked like or how these complex mechanisms arose? No, but they're looking for answers rather than their inquiry ending with Genesis.
===2. How did the DNA code originate?===
Scientists are actively investigating the genetic "code" and why it is what it is and how it might have emerged. Just like with abiogenesis, CMI tries to take the more complex genetic sequences in modern organisms and ask how something like this could spontaneously arise by sheer coincidence. This, of course, is scientifically ignorant and does not reflect what science actually says. There is a continuum of complexity. The likely precursor to the modern genetic code would be short strands of RNA that are autocatalytic (the chemical structure of the RNA strand produces a byproduct of itself). The "code" in this case is a basic copy and paste; there is no complex language or syntax. Since the odds of this early genetic code arising spontaneously are very high, CMI ignores it. 
The question of how the modern code emerged from these early predecessors is evolution itself. Random deviations in the nucleic acid structure would change the byproduct produced; if the byproduct was more efficient at replicating, it would overwhelm less efficient codes. This gradual change in the complexity of the underlying code is useful in explaining many aspects of biological theory, such as why RNA is used as an intermediate between DNA and protein synthesis. 
More generally, this highlights a common theme in all of these questions. CMI demonstrates a fundamental lack of understanding of the basic science behind the concepts they claim to be poking holes into. They butcher even the science that has nothing to do with evolution or that they should have no conflict with. In this case, their understanding of the "DNA code" refers to the way specific nucleic acid sequences on the DNA strand "code" for specific amino acids in the formation of proteins. The phrase "with letters and words where the meaning of the words is unrelated to the chemical properties of the letters" is laughably ignorant and shines a bright light on how the biased thought process of CMI is deadly to scientific advancement. Metaphors like "code" and "language" are simple tools that allow us to more easily grasp the basics for what might be going on, but they are just that — metaphors. But because CMI is assuming an intelligent designer, they make the mental leap that the metaphors have some sort of reality outside of our own mental constructs. This leads them to think that somehow the "DNA code" can be separated from basic chemicals and biological pathways. 
In reality, the whole thing is completely based on chemical properties. A specific sequence of nucleic acids in the DNA chemically bonds to a specific sequence of nucleic acids in an RNA strand, which in turn chemically binds a specific amino acid. If we were to change the electrochemical properties of the nucleic acid, then the whole process would fall apart. You could describe the reaction between vinegar and baking soda as "the foam is a product of a communication between aggressive vinegar and the more passive baking soda in their effort to reach a more stable and comfortable environment." Most people could recognize this as a bit of a tortured metaphor, but not as an actual physical description of what is going on. People realize that there is a chemical reaction taking place that has nothing to do with communication or the internal emotional states of the chemicals. Someone who tried to argue that the common explanation of the reaction between baking soda and vinegar is false because there is no evidence that baking soda is emotionally passive would be laughed at. 
And that is why we laugh at CMI when they try and take the metaphoric language scientists sometimes use and turn it around into a scientifically illiterate argument against evolution.
===3. How could mutations create the huge volumes of information in the DNA of living things? (about 6 gigabits, by CMI’s estimate)===
CMI again uses a lot of metaphors, such as "letters", "cookbook", "postman", and "parcels". Such metaphors are not used by geneticists because they are false analogies — CMI's sole purpose in using them is to create a false sense of intelligence at the cellular level. Also, referring to mutations simply as "errors" is slightly improper, and a better definition would have been "changes in the nucleotide sequence of a genome".
As an initial matter, the notion that the amount of "information" in a genome depends on its length is specious and reflects CMI's bad faith in presenting a question it knows is predicated on a false premise. Elsewhere, CMI describes the concept of "information" as describing a specific genetic instruction, though it's very difficult to know what special significance CMI gives to one such instruction over another and why one would contain more information than any other. Nonetheless, CMI admits that genotypes are determined by instructions in individual and combinations of codons, which on its own reflects CMI's insincerity in claiming the amount of information is determined by the length of a genome. This claim is empirically, observably incorrect — Amoeba proteus, which CMI would certainly consider a simpler or lower form of life than Homo sapiens, and which does objectively have a much simpler biochemistry than us, has a genome including about 290 billion base pairs — nearly 100 times the size of the human genome. As CMI also admits that there is a good amount of non-coding DNA, though some of it may have some non-coding function, so CMI ought to know that its description of 3 billion ACGT's being "information" is scientific gibberish and inconsistent with other scientific gibberish it has advanced elsewhere about "information".
Accepting for purposes of discussion CMI's meaningless estimate of an amount of "information" based on the length of the genome, we do know that the first living cells appeared roughly 3 billion years ago, which gives plenty of time for mutations. If only eight mutations occurred per year that were subsequently passed down to the present day, that's 3 gigabytes of variation. Evolution does depend on mutations, and these do appear to be random. Cumulative mutations may become significant factors for an organism once pitted against the dynamics of its environment. Thus, natural selection isn’t random; it’s deterministic. Many creationists will even admit this. And as some computer models have already shown, natural selection can actually even exceed the skills of human designers. In fact, natural selection can be so deterministic that it often leads to innovations which some perceive as evidence of intelligent design, and which even rationalists describe as having the appearance of having being modified for intended benefit.
Creationists insist that mutations are very rare and are usually, if not always, harmful. But the fact is that the vast majority of mutations are completely neutral and have minimal effects. Harmful mutations are those such as a deletion mutation or an addition mutation, e.g. removing or adding a nucleic base. They’d have to be because, according to the National Center for Biotechnology Information, there is an overall average of 128 mutations per human zygote!http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288368/ So apparently, in creationist terms, "very rare" means "more than a hundred per person right from the point of conception". Because those are just the mutations we start out with. Our cells will mutate again 30 more times over the course of our lives, and some of these subsequent mutations can be passed on to our children, too – usually with no more effect than those we recognize as family traits. Large additions of genetic information occur when genes or even whole chromosomes or genomes are duplicated and these duplications are inherited. This is why there are structural similarities between the chromosomes found within each cell. They have been duplicated from one another.
===4. Why is natural selection taught as "evolution", when natural selection selects, but does not create?===
This question is not even wrong. Nobody claims that evolution is a spontaneous creative process — see the answer to question 1. It is not concerned with addressing "goo-to-you". It is capable of explaining the extraordinary variety of living things, including finches and their beaks. As creationists accept, natural selection is about testing the fitness of new traits arising from mutations, which, if they provide an advantage, become distributed through the population of organisms. While mutations are random and at first blush appear incapable of creating new traits that last, natural selection is a highly creative mechanism: the effect of culling organisms whose mutations render them less fit is to concentrate successful mutations that provide an advantageous adaptation against selective pressures in the remaining population.
Though they have no non-frivolous objection to the proposition, creationists will not accept that the cumulative effect of natural selection is the substantial morphological variety we see in living organisms and the fossil record. Despite the fact that CMI and its adherents downplay their previous use of "microevolution", which they accept, and "macroevolution", which they don't, they continue to implicitly rely on some unstated distinction between the terms in denying universal common descent. The real question is, despite their acceptance of the basic function of natural selection to create variety (albeit only within "kinds" according to creationists), why are they more prepared to accept a biblical explanation riddled with more serious problems than authorship, provenance, or accuracy that raises more questions than it answers over the compelling 
Biological evolution is both variation through mutations and natural selection; hence, the understanding of both is important for evolution. Since the creationists emphasized mutations in the previous question as a part of evolution, why do they ignore it now?
===5. How did new biochemical pathways, which involve multiple enzymes working together in sequence, originate?===
First of all, this question commits the logical fallacies: argument from ignorance and personal disbelief.
Second of all, as stated on Talk Origins:
and
In fact, just the most cursory of searches in the scientific literature reveals dozens of peer-reviewed publications in exactly this field.Chapman, D.J. and Ragan, M.A. (1980). Evolution of Biochemical Pathways: Evidence From Comparative Biochemistry. Ann. Rev. Plant Physiol. 31: 639-67.Whitaker, R.J., Berry, A., Byng, G.S., Fiske, M.J. and Jensen, R.A. (1984). Clues from Xanthomonas campestris about the evolution of aromatic biosynthesis and its regulation. J. Mol. Evol. 21: 139-49.Jensen, R.A. (1985). Biochemical Pathways in Prokaryotes Can Be Traced Backward through Evolutionary Time. Mol. Biol. Evol. 2: 92-108.Ahmad, S. and Jensen, R.A. (1987). Evolution of the biochemical pathway for aromatic amino acid biosynthesis in Serpens flexibilis in relationship to its phylogenetic position. Arch. Microbiol. 147: 8-12.Forst, C.V. and Schulten, K. (1999). Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information. J. Comp. Biol. 6: 343-63.Behrman , E.J., Marzluf, G.A. and Bentley, R. (2004). Evidence from Biochemical Pathways in Favor of Unfinished Evolution rather than Intelligent Design. J. Chem. Educ. 81: 1051.Koes, R., Verweij, W. and Quattrocchio, F. (2005). Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 10: 236-42.Nacher, J.C., Ochiai, T., Yamada, T., Kanehisa, M. and Akutsu, T. (2006). The role of log-normal dynamics in the evolution of biochemical pathways. Biosystems' 83: 26-37.Raymond, J. and Segrè, D. (2006). The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life. Science 311: 1764-1767.Harborne, J.B. (2008). Constraints on the evolution of biochemical pathways. Biol. J. Linn. Soc. 39: 135-151.Fani, R. and Fondi, M. (2009). Origin and evolution of metabolic pathways. Phys. Life. Rev. 6: 23-52. So while creationists might consider this to be a deep and intractable mystery, it seems that the professionals who've dedicated their lives to training and working in these areas do not.
Thirdly, the implication that such metabolic pathways arose solely by "lucky accidents" can only demonstrate a lack of understanding of evolution, or perhaps dishonest intent. Scientists do not claim that evolution is a random process because the random element of mutation is shaped by the distinctly non-random process of natural selection.
Fourthly, looking at the biochemical processes in detail at a moment in time does not indicate the evolutionary history of an organism. Scaffolding is a means to develop a process. Furthermore, evolution is established on the macroscopic level through morphology as well as on the molecular level with genetics. As the understanding of biochemistry proceeds (as it is a much younger science), a better understanding will develop. Instead of attempting to generate evidence to demonstrate that such pathways cannot evolve, creationists merely assert that they cannot, and then expect to be taken seriously. As Michael Behe learned at the Dover trial, his assertion that complexity cannot evolve was overwhelmingly unsubstantiated, for there is a lot known about the evolution of proteins, such as with the immune system. 
Furthermore, we've observed the appearance of such discrete functions in the present day both in the laboratory and in the wild. The Lenski experiment demonstrates that, with time and proper mutations, completely new pathways do in fact, provably, originate. Of course, such systems didn't appear fully formed, but evolved gradually by discrete steps that built on pre-existing metabolic functions to provide competitive advantages to their organisms. In the Lenski experiment, we've observed the development of the ability to utilize citric acid as an energy source in bacteria grown under the appropriate selective pressures;Lenski, R.E. (2004). Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Plant Breed. Rev. 24: 225-265. and in the wild, we've observed the appearance of novel enzymes capable of allowing bacteria to utilize nylon oligomers as carbon sources.Ohno, S. (1984). Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence. Proc. Natl. Acad. Sci. USA 81: 2421-25. Furthermore, in the latter case, this evolution has not only been replicated in the laboratory, but two new and distinct nylonase enzymes have been identified in one bacterium in the wild,Okada, H.et al. (1983). Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature 306, 203-206. therefore clearly showing the evolution of a two-step pathway in barely one human lifetime. With such demonstrable and empirical evidence in hand, how big a leap is it really to imagine the evolution of more complex pathways over periods measured in billions of years?
Finally, notice that the quote provided by Franklin Harold starts with a lowercase "w": this is because the creators of these 15 Questions left out the rest of the quote, and yes, it is a deliberate quote mine. The quote on page 205 in Harold's book, The Way of the Cell, is preceded by the words: “We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity but…”
===6. Why do living things bear the hallmarks of design, if no one designed them?===
They don't. The claim that living things bear the hallmarks of design is, at best, a mere assertion based on the argument from ignorance that evolution's supposed failure to explain biological complexity, labeled as "too much design", necessarily entails a designer. It doesn't. If there is a designer who created this universe, then that designer is clearly imperfect because of the abundance of natural disasters and microbial life that can inflict death and disease on its victims. Clearly such design is imperfect. Creationists love to point to the seemingly "beautiful" appearance of DNA as evidence for design, yet they ignore the existence of genetic defects that can kill fetuses or condemn people to an early death. Obviously, life-threatening genetic anomalies in innocent babies are not evidence of a perfect creator.
Despite creationists' subjective characterization of the appearances, their claim of the existence of a designer does not logically follow from evolution's perceived lack of explanatory power. As Kenneth Miller puts it, the illusion of design to a creationist is 
Richard Dawkins is addressing the pervasive illusion of design in the quote CMI uses. CMI omits Dawkins' long explanation of why biological complexity does not require a designer, which is a central premise of The Blind Watchmaker. Francis Crick is also here expressing his awareness of our innate tendency to to unguided physical processes. And it's really no wonder that scientists are vigilant against indulging the innate human bias toward assuming complexity entails design. After reading On the Origin of Species, which details Darwin's explanation of how the unaided laws of physics could mimic design, Thomas Huxley exclaimed "How extremely stupid not to have thought of that."From Natural History Magazine, Introduction: The Illusion of Design
Were one to play the game of supposing what an intelligent designer would do, it would at least be according to the familiar principle that designs should strive for simplicity, not complexity. Yet, this is the opposite of what we see when we examine things closely. The great variety of complex biological structures is the kind of accident you'd expect to happen with an unguided process like evolution rather than if someone carefully put organisms together from scratch. Thus, in presuming to ascribe motive to a designer, one actually finds examples of bad design.
Nonetheless, science isn't concerned with ascribing motives to physical processes, but with providing naturalistic explanations. Thus, it's odd that CMI makes an unstated distinction between "naturalistic causes" and "logical causes" when the success of Intelligent Design Creationism as a scientific theory depends on its ability to identify purported design consistent with the scientific method, i.e. by providing naturalistic explanations. One then assumes that "logical causes" is a code word for goddidit, which is an argument from ignorance — an argument which is not a tool available to science (and for very good reason). Scientists don't reject goddidit a priori out of some dogmatic bias against religion. Science is concerned with naturalistic explanations because invoking the supernatural violates Occam's razor by raising more questions than it answers. That is why science should be "restricted to naturalistic causes rather than logical causes." Or, as Richard Dawkins put it:
===7. How did multi-cellular life originate?===
It was beneficial for single-celled organisms to work together. For instance, mitochondria, the "power sources" of cells, were once separate organisms. Other cells benefit from their ability to generate power while the mitochrondial cells benefit from a constant stream of food supplied to them by the larger organism. "The intermediate stage between one-celled and multicelled life need not have been two-celled. The first requirement is for signals between cells, which is necessary if cells are to cooperate in division of labor to break down a food source. Many bacteria utilize a variety of different signals. The evolution of a signal for cooperative swarming has been observed in one bacterium.Talk Origins cites Velicer, G. J. and Y. N. Yu. 2003. "Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus." Nature, 425, 75-78."http://www.talkorigins.org/indexcc/CB/CB922.html 
"The transition to multicellularity has been studied in experiments with Pseudomonas fluorescens, which showed that "transitions to higher orders of complexity are readily achievable".Talk Origins cites Rainey, Paul B. and Katrina Rainey. 2003. Evolution of cooperation and conflict in experimental bacterial populations. Nature 425: 72-74. Choanoflagellates, which are unicellular and colonial organisms related to multicelled animals, express several proteins similar to those used in cell interactions, showing that such proteins could arise in single-celled animals and be co-opted for multicellular development.Talk Origins cites King, Nicole, Christopher T. Hittinger and Sean B. Carroll. 2003. Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301: 361-363."
"Desmidoideae is a class of conjugating green algae, phylum Gamophyta. Most desmids form pairs of cells whose cytoplasms are joined at an isthmus.Talk Origins cites 2. Margulis, Lynn and Karlene V. Schwartz. 1982. Five Kingdoms San Francisco: W. H. Freeman. The bacterium Neisseria also tends to form two-celled arrangements. As noted above, this may not be relevant to the evolution of multicellularity." Recent studies have shown that the jump to multicellular may not be as big a jump as once thought.http://www.newscientist.com/article/mg21028184.300-lab-yeast-make-evolutionary-leap-to-multicellularity.html
===8. How did sexual reproduction originate?===
"Sexual reproduction allows for evolution to occur at a much faster pace than asexual reproduction. Organisms that exchanged DNA were thus able to evolve out of situations that might have killed their asexual counterparts. The variety of life cycles is very great. It is not simply a matter of being sexual or asexual. There are many intermediate stages. A gradual origin, with each step favored by natural selection, is possible.Talk Origins cites Kondrashov, Alexey S., 1997. Evolutionary genetics of life cycles. Annual Review of Ecology and Systematics 28: 391-435. The earliest steps involve single-celled organisms exchanging genetic information; they need not be distinct sexes (in fact, modern bacteria do this today). Males and females most emphatically would not evolve independently. Sex, by definition, depends on both male and female acting together. As sex evolved, there would have been some incompatibilities causing sterility (just as there are today), but these would affect individuals, not whole populations, and the genes that cause such incompatibility would rapidly be selected against."http://www.talkorigins.org/indexcc/CB/CB350.html
===9. Why do the millions of "missing links" remain missing?===
They don't. Every fossil ever found is a link between older and newer forms. Anybody expecting to find a half crocodile-half duck in the fossil record, or indeed anywhere, doesn't understand evolution. There is no expectation of countless millions of transitional fossils. When something dies, it is usually disassembled, digested, and decomposed. Only rarely is anything ever fossilized, and even fewer things are very well-preserved.http://www.talkorigins.org/indexcc/CC/CC200_1.html Because the conditions required for that process are so particular, the fossil record can only represent a tiny fraction of everything that has ever lived. Darwin provided many environmental dynamics explaining why no single quarry could ever provide a continuous record of biological events, and why it would be impossible to find all the fossilized ancestors of every lineage. But despite this, he predicted that future generations, having the benefit of better understanding, would discover a substantial number of fossil species which he called "intermediate" or "transitional" between what we see alive today and their taxonomic ancestors at successive levels in paleontological history. So the whole "missing link" idea is hopelessly obsolete.
In fact, in the century and a half since then, we’ve found millions of evolutionary intermediaries in the fossil record, much more than Darwin said he could reasonably hope for. The transitional fossils that have been found (such as Tiktaalik, Ichthyostega, Australopithecus, Homo habilis, Archaeopteryx, Microraptor, Sinosauropteryx, Yutyrannus, etc.) provide clear evidence of transitions, in this case from water to land and from land to flight. There are three different types of transitional forms and we have ample examples of each. But creationists still insist that we've never found a single one, because what they usually ask us to present are impossible parodies which would, in fact, refute evolution (such as the Crocoduck).
A decade ago, Kathleen Hunt, a zoologist with the University of Washington, produced a list of a few hundred of the more dramatic transitional species known so far, all of which definitely fit every criterion required of the most restrictive definition.http://www.talkorigins.org/faqs/faq-transitional.html Myriad transitional species have been, and still are being, discovered — so many, in fact, that lots of biologists and paleontologists now consider that list "innumerable", especially since the tally of definite transitionals keeps growing so fast. Several lineages are now virtually complete, including our own. See also our list of transitional forms.
The citation of Stephen J. Gould is a blatant (and fairly typical) quote mine.
This line of questioning also appears to be ill-faithed because of the following argument: Suppose creationists are demanding the missing link between species A and B. If C is found to be the missing link between A and B, the creationists will demand the missing link between A and C and the one between C and B. Now there are twice the number of missing links to be demanded! This provides basically infinite room for their continued denialism regarding transitional fossils. This, in fact, is how we got to a position where we have millions of "missing links".
===10. How do "living fossils" remain unchanged while so many other life forms are supposed to have changed radically? (The classic examples: coelacanth, lemurs, horseshoe crabs)===
No longer is this considered as much of a problem as creationists might lead you to believe. Thanks to the works of Gould himself for developing the theory of punctuated equilibrium — which is based on positive evidence, including extensive studies of living and extinct species groups — the stability of a species isn't a barrier to evolution.Eldredge, Niles and S. J. Gould (1972). "Punctuated equilibria: an alternative to phyletic gradualism" In T.J.M. Schopf, ed., Models in Paleobiology. San Francisco: Freeman Cooper. pp. 82-115. Reprinted in N. Eldredge Time frames. Princeton: Princeton Univ. Press, 1985, pp. 193-223. Simply put: when creatures don't need to adapt to changing situations, they don't change (much). Punctuated equilibrium is a model where plenty of evolutionary change can happen rapidly due to (relatively) fast changes in the environment. Without this sort of selection pressure, there is little driving force to cause evolution to progress — it's simply not right to say that creatures should be constantly changing. 
However, there is some debate on the issue of punctuated equilibrium within the scientific community. Richard Dawkins, for example, is not convinced by the punctuated equilibrium hypothesis and has argued that the apparent long periods without change are simply an artifact of the fossil record. We know that fossilisation is a rare occurrence, and technically we're lucky to have any, so the alternative explanation is that long periods of slow change are simply smeared out in the evidence record and not recorded. However, such debate is exactly what one would expect in science — where facts are not set in stone from an ancient book, and evidence is gathered to refine views.
Evolution can also be more subtle than creatures dramatically changing. It's quite possible that while living fossils have identical exterior appearance (phenotypes), they have in fact changed their internal biochemistry fairly dramatically (genotypes). Proteins that carry oxygen in the blood, for example, can be slightly altered in structure to change their loading rates as a reaction to slowly changing oxygen levels — and yet the outward appearance of the organism may remain unchanged. (An example is the people of Tibet, whose bodies have adapted to tolerate low oxygen levels but in outward appearance they haven't changed much.) Certainly in the relatively large leaps in evolution observed in the lab, whether it be speciation of fruit flies or the Lenski experiment, massive changes in appearance aren't necessarily observed, but the change is instead confined internally.
Their example of the coelacanth is telling, and shows they haven't done their research. Coelacanths are an entire order of fish, not a single species. In fact, there are two different species living today, neither of which is the same as those we find in the fossil record. Coelacanths have changed over time; what was remarkable about their discovery was that they still existed at all — it was thought that the entire order had died out. For comparison, the order that humans belong to is primates, and certainly even YECs will agree that we're substantially different from, say, chimpanzees, and we and chimps are both very different from, say, lemurs.
===11. How did blind chemistry create mind/intelligence, meaning and morality?===
This is an argument from adverse consequences and a straw man. Evolution makes no statement about the existence of God. The concept of "God" is irrelevant to the theory of evolution, and so is morality or the meaning of life. Creationists should know this, but they shamelessly repeat this nonsense at every opportunity. Although the theory of evolution does not necessarily refute God (or gods or fairies), it certainly and clearly does away with a literal belief in the book of Genesis. And this is what creationists are really trying to defend: an infallible authority of a story that tells us that the Universe was the product of magic. 
Intelligence is simply an evolutionary trait.http://www.talkorigins.org/indexcc/CB/CB400_1.html Its development has led to humans becoming one of the most successful species on the planet.Depending on the definition of "success". Time will tell what species comes out "on top". Meaning and morality are entirely human-generated concepts.
Furthermore, organisms develop from egg to full organism all the time through "blind" chemistry. Is that a problem?
===12. Why do evolutionists tolerate the telling of "just-so" stories in their work?===
The examples quoted from Skell are genuine problems with evolutionary psychology, which tends to give oversimplified explanations of human behaviour. But generalizing them to all of evolutionary study is a straw man argument.
Evolution's "just-so" story is based on facts, unlike any of the world's religions' form of creationism (remember, it's not just evolution or Genesis; Hinduism and other world religions have creation stories, each as valid as Christianity's (at least to anyone not predisposed to regarding their religion as right and every other religion as wrong)). Evolution with natural selection is the only explanation of biodiversity with either evidentiary support or scientific validity. There has only ever been one alternative theory against it, and it was an earlier version of evolution (Lamarckism). 
No branch of creationism has ever met even one of the criteria required of a theory. They can't meet the criteria because science demands both accuracy and accountability. So there has to be a way to detect and correct any errors in a given explanation, and determine for certain whether it's wrong in whole or in part, or whether any of it is true to any degree at all. A theory has to be tested indefinitely. It demands understanding instead of belief. So it must be based on verifiable evidence; it must explain related observations with a measurable degree of accuracy; it must withstand continuous critical analysis in peer review; and it must be falsifiable too. If it doesn't fulfill all these conditions at once, then it isn't science. If it meets none of them, it may be religion.
===13. What scientific breakthroughs resulted from evolutionary theory?===
Evolution is an extraordinary breakthrough in its own right. It explains how, through a series of simple steps, every living thing on the planet came into existence. These days, evolutionary concepts are being applied to fields such as electronics to help create efficient circuits. In computer science, genetic algorithms (GAs), which are based on evolutionary concepts, are very effective in many kinds of applications — for a simple illustration, see Dawkins weasel. (Dembski disagrees, of course, but he didn't exactly understand the point of using GAs to begin with, as our discussions of his papers show.) There are many evolutionary breakthroughs, and the first person this pamphlet provided admitted it. As for the second, he forgets evolutionary theory is not only beneficial to medicine (we often give antibiotics in group regimens, a practice called multidrug therapy, because we understand the mechanisms by which drug resistance — a major public health issue, see e.g. MRSA — develops and how to delay or prevent it) but also agriculture. In 1970, Norman Borlaug was awarded the Nobel Peace Prize because his understanding of the theory of evolution and genetics helped him mass produce crops to feed millions of people. Also, evolutionary psychology and neuroscience investigates the complexity of biological characteristics that give rise to psychological disorders and neurotic behaviors by developing an understanding of evolution. Evolutionary psychology examines psychological traits such as memory, perception, and language from a modern evolutionary perspective.
The quote from Dr. Skell is a prime example of an appeal to authority. That is to say that as a chemist, he is speaking outside his fieldPanda's Thumb on Dr Skell when he refers to evolution. is a distinct field, and there is a journal devoted to molecular biology and evolution.Molecular Biology and Evolution. Any study of DNA sequences over time or sequence comparison between organisms could be considered evolution biochemistry or molecular biology. And because Dr. Skell's field of work does not actually deal directly with anything biological, he is an inappropriate authority to appeal to, and Skell's assertion about is unsupported. The distinction between "experimental biology" and "evolution" is a straw man, as there are experimental instances of evolution.
But of course, the main issue is that the usefulness and applicability of a theory has nothing necessarily to do with its correctness and accuracy. Besides, if evolution is so unimportant, why discuss it in the first place? And, more telling: what breakthroughs has creationism produced? Or Intelligent Design, for that matter. See, the whole point of a scientific framework is that you can use it to launch other inquiries — if you stop at "God did it" or "someone designed/built it", you have nowhere to go, nothing to build new inquiries on.
===14. Why is evolution taught as operational science, when it does not involve true experiment?===
There have been plenty of experiments carried out that demonstrate evolution. One of the most famous is one carried out by professor Richard Lenski, which led to so many creationist red faces and escape hatches.
The fact that CMI refuse to accept the results tells us a lot about CMI but little about evolution. Evolution can be observed and tested right now.The species that can be tested in situ is usually limited by any bioethics regulations. You certainly can observe what happened in the past. If you come across a crime scene, detectives observe and test all the available evidence to come to the truth. The fossil record and genetics provides us with an observation of what happened in the past. Creationists ask for evidence that we descended from apes — when the most obvious evidence for this is that even the algorithm developed by the creationist Carl Linnæus classified us as apes.
===15. Why is evolution accepted and taught as science when in fact it cannot explain the evidence?===
It can. CMI simply refuses to acknowledge this. Evolution is not dogmatic or a fundamental religious idea. Evolution is the branch of science (biology) which explains biodiversity. Science itself doesn’t make use of supernatural explanations, has no doctrines nor dogma, and it doesn’t require nor allow blind faith. It holds nothing sacred; it neither promotes nor discourages belief in gods or souls, and says nothing about how we should live or what happens after we die. Evolution is therefore not a religion, and creationists know it's not — but they say it is anyway, because they see it as a threat to their worldview. In creationists' defence, they might need some education to become competentSee Clarke's third law. to verify the results. But the point of science is that anyone with the right tools, safety equipment, and skills can reproduce the results.
Popper's use of the word "metaphysical", contrary to the hopes lies of creationists, does not mean religious, but rather refers to an untestable idea that still leads to testable predictions (the explication of "metaphysical research programme" as "a possible framework for testable scientific theories" occurs in the same fucking sentence as the mined quote). Popper also said of evolution: "And yet, the theory is invaluable. I do not see how, without it, our knowledge could have grown as it has done since Darwin. In trying to explain experiments with bacteria which become adapted to, say, penicillin, it is quite clear that we are greatly helped by the theory of natural selection. Although it is metaphysical, it sheds much light upon very concrete and very practical researches. It allows us to study adaptation to a new environment (such as a penicillin-infested environment) in a rational way: it suggests the existence of a mechanism of adaptation, and it allows us even to study in detail the mechanism at work. And it is the only theory so far which does all that."Talk Origins Index of Creation Claims CA211.1 Popper on natural selection's testability Popper also later changed his mind on the testability of natural selection: "I have changed my mind about the testability and logical status of the theory of natural selection; and I am glad to have an opportunity to make a recantation."http://atheism.about.com/b/2006/06/20/karl-popper-and-evolution-is-evolutionary-theory-based-on-a-tautology.htm
The quote from Michael Ruse is misleading, and comes from an article in the National Post entitled, in part, "How Evolution Became a Religion". Nearing the end he mentions: "There is no need to make a religion of evolution. On its own merits, evolution as science is just that — good, tough, forward-looking science which should be taught as a matter of course to all children, regardless of creed. But, let us be tolerant. If people want to make a religion of evolution, that is their business."HOW EVOLUTION BECAME A RELIGION Creationists correct?: Darwinians wrongly mix science with morality, politics Saturday, May 13, 2000 — National Post By MICHAEL RUSE Further, he mentions, "The important point is that we should recognize when people are going beyond the strict science, moving into moral and social claims, thinking of their theory as an all-embracing world picture." Ruse is differentiating between evolution as purely science and evolutionism as a belief system. 
Clarifying such a distinction even further, in Science Magazine, Ruse talks about how creationists accuse evolution as being more than a scientific theory, and goes on to talk about the history of the theory of evolution. His concluding comments pertaining to what the history teaches us are as follows:Science 7 March 2003: Vol. 299 no. 5612 pp. 1523-1524
Ruse objects when, in his words, "evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion." Ruse argues that anyone who does this should be careful to distinguish between science, and philosophical viewpoints based on science.http://www.talkorigins.org/faqs/homs/iconshe.html 
The foregoing highly suggests creationists here are ignoring (or are ignorant to) the context of Ruse's quote and the background of his ideas, making a strawman argument out of his words. He was talking about popular evolutionism as a religion, not evolution taught as a science.
==See also==
*Gish Gallop
*Just asking questions
*Question Creationism! A response.
*Traditional Values Coalition
==External links==
*Question Evolution Pamphlet
*Question Gravity: 15 Questions for Gravitationalists, Join the worldwide Question Gravity campaign!
*FABNAQ (Frequently Asked But Never Answered Questions) at TalkOrigins
==Notes==
==References==
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