The Language of God is an interesting read from one of the world's most prestigious scientists. He recounts his own conversion from agnosticism to theism, and goes on to examine how a personal creator accords with the findings of science. This book could be very helpful to non-believers when questioning their own agnosticism or atheism. I found it less useful as a guide to a Christian view of origins.
Collins' Objections to 'God of the Gaps' Arguments
Collins says, "Faith that places God in the gaps of current understanding about the natural world may be headed for crisis if advances in science subsequently fill those gaps."1 This is an oft-repeated point in other's work, and has a lot of history behind it. However, there are gaps which should be filled in our understanding by God. Every time a miracle happens, we have something we don't understand. And God is the explanation. Every act of God in history is a gap that, properly understood, is filled with God. While it's easy to err and attribute to God's intervention things that have natural causes, this only means we should be careful. It does not mean that gaps in scientific knowledge may indeed be answered best by divine intervention.
Collins is eager to avoid giving God as the reason for unexplainable things in natural history. But what is the difference between seeing God in the unbridgeable gap between simple organic compounds and living cells on one hand (which Collins resists), and between the big bang and whatever happened beforehand on the other (which Collins accepts)? Using a God of the gaps argument seems to be okay in some situations, but the rules are unclear.
Referring to inorganic evolution and why it would be unwise to assume God is responsible, he says,
There are good reasons to believe in God, including the existence of mathematical principles and order in creation. They are positive reasons based on knowledge, rather than default assumptions based on (a temporary) lack of knowledge."2
He seems to believe that science will soon explain inorganic evolution also, so we shouldn't attribute it to God. I thought this position was way too cautious.
Discussing the Cambrian explosion, he says,
While attempts have been made by certain theists to argue that the Cambrian explosion is evidence of the intervention of some supernatural force, a careful examination of the facts does not seem to warrant this. This is another "God of the gaps" argument, and once again believers would be unwise to hang their faith upon such a hypothesis."3
I see no argument or evidence given here to back this rejection of divine intervention at or around the Cambrian explosion. Whether the theistic position is a 'gaps argument' begs the question and is ad hominem. Ad hominem means "against the man" where instead of refuting one's evidence, you point out he is making a similar argument to a discredited other (like Hitler), or in this case, earlier mistaken Christians. It's an invalid form of argument, because the fact that someone else messed up when using a similar argument means nothing about whether the present case is messed up.
The fact is that our observable data show huge discontinuities in the fossil record appearing in short time spans. Of course we can speculate about possible explanations that would still allow for the slow transitions required by Darwinian Theory, but such speculations have no backing in observable data, and cannot be considered science. This is particularly hard to accept when layers of sediment (like limestone) from the same ocean show change happening between one layer and another. Why would the ocean stop depositing sediment and then start again? In cases where the ocean dried up for a period and re-filled (which has happened numerous times with shallow inland seas) you can see clear signs that this is what happened.
The only argument I could see by Collins was that "The so-called Cambrian explosion might, for example, reflect a change in conditions that allowed fossilization of a large number of species that had actually been in existence for millions of years,"4 How is this explanation for the gap any different or any better than the hypothesis that God intervened at this point in history? I agree with him that we cannot be dogmatic on such ancient issues. I also agree that people shouldn't "hang their faith" on the assumption that God intervened here. But the theistic hypothesis seems far more plausible to me than some worldwide change in fossil formation capability. An appeal to some change in the way fossils form, which formerly allowed microscopic fossils, but afterward allowed larger, complex fossils seems rather desperate to me. Normally larger organisms form fossils most easily. He gives no clear description of how this change would happen, or why.
Atheists argue that people have erroneously used the 'God of the gaps' argument before, and therefore we should never use it again. Similarly, amillenialists ague that people have erroneously argued that the end times are at hand based on so-called 'signs,' so we should never again argue that case. Both of these are fallacious arguments.
Just because God was wrongly blamed for being the cause of certain gaps in understanding (like what causes disease) doesn't mean there are no gaps that should be attributed to God. This would lead to a completely naturalistic worldview. Miracles would be impossible. All apparent interventions by God would have to be left in abeyance in the belief that someday science will explain it.
Collins doesn't deny the reality of miracles, and in fact says he believes in them. But his method makes it necessary to prove something is a miracle before believing in it. Many miracles can't be proven, but are real. I'm not commenting on Collins' beliefs here, I'm commenting on his methodology.
Likewise, just because people argued falsely that the end times were at hand based on signs that were misinterpreted doesn't mean that the end times won't be signaled by signs correctly interpreted, as Jesus clearly teaches in the parable of the fig tree (Mat. 24:32, 33). Such ad hominem arguments would be analogous to saying that since evolution was the basis for National Socialism and communism; we should never appeal to evolution for any explanations.
In a word, the fact that people have used a line of reasoning poorly in the past doesn't mean the line of reasoning is discredited—only their improper use of it. Collins himself has suggested at least one gap that should be attributed to God (the big bang), and grudgingly admits that another (inorganic evolution) could be explained by God. As biblical theists, we believe there are many gaps that should be explained by God's action in history.
Macroevolution and the fossil record
Collins' rejection of the distinction between macro and microevolution (p. 132) is based on an overly narrow definition of microevolution. I agree that Christians often err here, by claiming that no new species have appeared through evolution. The evidence is good that many species are the result of evolution. I have always held that in the expression, "after its own kind," (Gen. 1) the word 'kind' is not defined. It could mean species, genus, family, or even phyla or something larger. I also agree with Collins that the idea of macroevolution has no clear definition and is therefore a somewhat vague concept. But I think it is still useful for declaring that evolution has some limits in what it can explain. "Reproducing after its own kind" has to mean something. The rules of exegesis say you can't just ignore language that doesn't fit your theory. If the amoeba gave rise to humans, then what does "reproducing after its own kind" mean? The phrase seems to be saying there were limits within which organisms reproduce. If not this, what does it mean?
Collins never adequately addresses the larger question of jumps in the fossil record. Even the discovery of some possible transitional forms (where formerly there were none) cannot be reasonably extrapolated to mean that all missing transitions will eventually be found, or that they once existed, but were never preserved in the fossil record. This is a faith position without observable backing. It fills the gaps with imagined fossils that have never actually been seen. It also fails to speak to the stability of species in the fossil record, where most species appear relatively suddenly, stay very stable throughout their history (except for minor changes like size) and then often disappear. This picture does not fit Darwinian assumptions. Think of the famous case of the horse. The changes seen in the fossil record are basically a change in size, which is qualitatively different than the kind of changes one would need to see in order to demonstrate macro-evolution.
Collins' proposition (that transitions may have occurred during periods when fossils were not deposited) means that such suspensions in fossil deposition would have to happen worldwide even in very different sedimentary strata, deposited in different ways. For instance, some are deposited by oceans, some by rivers, and some fossils come from animals trapped in tar pits or amber, to name a few. These would all have to suspend fossil making for many millions of years at the same time in order to explain why the discontinuous layers we have are really continuous and relatively constant in rate of change, as predicted by Darwin. Why would this happen? I think this is a huge leap of faith, and even atheist paleontologists like Gould use this same data to back up the need for punctuated equilibrium (which is leap of faith in itself).
The last research I did on this about three years ago indicated that only a handful of debatable links have been found, and that thousands of gaps remain as striking as ever. Robert Carroll observes recently in Nature, "What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types."5 Even in cases where possible transition fossils have been discovered, they are usually far distant from either the parent line, or the line they are supposed to explain, and authorities disagree on whether many of them are really transitional forms at all.
His efforts to argue that fossils are rare and the record extremely fragmentary is unconvincing. At every geological period, millions and even billions of fossils survive. The problem (not acknowledged or discussed by Collins, except in the case of the Cambrian explosion) is that strata containing abundant fossil remains from entire new orders lie immediately adjacent to strata containing none of these organisms or anything similar. This widespread phenomenon remains a major problem for Darwinian theorists. Collins' general statements about the difficulty of making fossils did nothing to answer this problem. Of course only a minority of organisms are ever preserved in fossil form. But as anyone who has studied fossils knows, this minority still usually numbers in the millions for most categories.
I believe his claim that the former view (that there were huge gaps all over the place) has now been refuted, is wrong. Authorities writing recently still argue that most significant gaps remain. The sudden appearance of new phyla, genera, and families is remarkable today as it has been. The only place I have seen such sweeping claims that the problems with fossils are not in the past is on atheist websites with low credibility.
Collins does not demonstrate careful study of the fossil record (geology and paleontology are not his area of expertise), and this is a serious weakness in his argument. Fossils remain the only objective data we have for what actually happened. Mathematical extrapolations from genetics does not stand, in my view, at the same level of credibility as the actual history as seen in the fossil record.
I admit that an explanation could conceivably be found one day for the discontinuities in the fossil record. But I believe the evidence today still conforms to a picture of periodic dramatic changes in plant and animal populations, and these are used to date sedimentary strata, because other strata are missing these forms. This picture is not easily explained by pure natural selection, and could indeed represent creative episodes where God intervened.
Interpreting molecular similarities
Collins shows compelling evidence for similarity between human and mouse DNA, even in non-functional sections. His conclusion is that such similarity denotes common ancestry. But while similarity could denote a common ancestor, it could also denote a common maker. Is it reasonable to assume that God would start from scratch every time he introduced a new order of organisms (assuming this happened)? Or would he begin with existing forms, and alter them in meaningful ways to produce the new order? I don't know how we could answer these questions. Clearly, if the notion that God periodically introduced new forms is true, the evidence suggests that he used existing forms as templates from which to build the new forms. This could explain the data just as well as evolution.
As an analogy, consider the way programmers produce a new computer program. They normally do not begin from scratch, but use helpful strings of code from previous programs they have written for various functions. Likewise, a Bible teacher will commonly include illustrations and arguments he has used in earlier teachings when constructing a new one. These similarities don't imply that the new program or teaching sprang from the former, but that the creator of both used existing material combined with new material to produce the new creations.
Collins admits that these similarities are only found "over substantial stretches" and "in some instances."6 He also concedes that, "one might argue that the order of genes is critical in order for their function to occur properly, and therefore a designer might have maintained that order in multiple acts of special creation."7But he feels that, "there is no evidence from current understanding of molecular biology that this restriction would need to apply over such substantial chromosomal distances." In other words, the similarity of sequence is longer than necessary for the functions involved. But this observation doesn't rule out the use of even relatively long similar chains by a designer. It only shows that such borrowing would not be necessary as far as we know. Indeed, understanding of the function of non-coding sections of DNA is constantly growing.7b
He concludes: "this kind of recent genome data thus presents and overwhelming challenge to those who hold to the idea that all species were created ex nihilo." I think this conclusion is warranted. But it may be a bit of a straw-man as well. Only extreme creationists continue to hold that all species were specially created. I fail to see why believers would argue this extreme position. However, the genome data do not present an overwhelming challenge to the view that God engaged in multiple creative acts at various points, combined with evolution.
Collins' work on biblical exegesis
Collins says, "The concern about not accepting liberal interpretations of biblical texts is understandable."8 But he also says, "…parts of the Bible, such as the first few chapters of Genesis, the book of Job, the Song of Solomon, and the Psalms, have a more lyrical and allegorical flavor, and do not seem to carry the marks of pure historical narrative."9 He adds, "to most other interpreters throughout history, until Darwin put believers on the defensive, the first chapters of Genesis had much more the feel of a morality play than an eyewitness report on the evening news."10 His view here only reflects Roman Catholic allegorizing during the medieval period, which was not only applied to these passages but to most historical narrative in the Bible. Allegorical hermeneutics were rejected well before Darwin by evangelical interpreters, and for reasons different than that assumed by Collins.11
These statements clearly signal that Collins has a view of scripture deemed unacceptable to the vast majority of evangelical scholarship and contrary to our own statement of faith. Consider the following articles from the "Chicago Statement on Biblical Hermeneutics" that are violated by these statements (key phrases that I think are denied are in bold):
WE AFFIRM that the Bible expresses God's truth in propositional statements, and we declare that biblical truth is both objective and absolute. We further affirm that a statement is true if it represents matters as they actually are, but is an error if it misrepresents the facts.
WE AFFIRM that awareness of the literary categories, formal and stylistic, of the various parts of Scripture is essential for proper exegesis, and hence we value genre criticism as one of the many disciplines of biblical study.
WE DENY that generic categories which negate historicity may rightly be imposed on biblical narratives which present themselves as factual.
WE AFFIRM the necessity of interpreting the Bible according to its literal, or normal, sense. The literal sense is the grammatical-historical sense, that is, the meaning which the writer expressed. Interpretation according to the literal sense will take account of all figures of speech and literary forms found in the text.
WE DENY the legitimacy of any approach to Scripture that attributes to it meaning which the literal sense does not support. [such as allegory—Dennis]
WE AFFIRM that since God is the author of all truth, all truths, biblical and extrabiblical, are consistent and cohere, and that the Bible speaks truth when it touches on matters pertaining to nature, history, or anything else. We further affirm that in some cases extrabiblical data have value for clarifying what Scripture teaches, and for prompting correction of faulty interpretations.
WE DENY that extrabiblical views ever disprove the teaching of Scripture or hold priority over it.
WE AFFIRM that Genesis 1-11 is factual, as is the rest of the book.
WE DENY that the teachings of Genesis 1-11 are mythical and that scientific hypotheses about earth history or the origin of humanity may be invoked to overthrow what Scripture teaches about creation.
Also note these statements from the "Chicago Statement on Biblical Inerrancy:"
4. Being wholly and verbally God-given, Scripture is without error or fault in all its teaching, no less in what it states about God's acts in creation, about the events of world history, and about its own literary origins under God, than in its witness to God's saving grace in individual lives.
We affirm that Scripture in its entirety is inerrant, being free from all falsehood, fraud, or deceit.
We deny that Biblical infallibility and inerrancy are limited to spiritual, religious, or redemptive themes, exclusive of assertions in the fields of history and science. We further deny that scientific hypotheses about earth history may properly be used to overturn the teaching of Scripture on creation and the flood.
[Their point here is that we begin with exegesis and determine the limits allowed. THEN we go to science as it stands today to see what is more or less likely within those limits. The wrong approach would be to reach conclusions via science, and then make scripture fit that conclusion—which is exactly the approach Collins takes when he dismisses Gen 1-11 as history. – Dennis]
We affirm that the doctrine of inerrancy has been integral to the Church's faith throughout its history.
We deny that inerrancy is a doctrine invented by scholastic Protestantism, or is a reactionary position postulated in response to negative higher criticism.
We affirm that the text of Scripture is to be interpreted by grammatico-historical exegesis, taking account of its literary forms and devices, and that Scripture is to interpret Scripture.
We deny the legitimacy of any treatment of the text or quest for sources lying behind it that leads or relativizing, dehistoricizing, or discounting its teaching, or rejecting its claims of authorship.
I think Collins' approach to scripture violates all of these statements, and is completely unacceptable for Bible believers. Such a view could prove a stumbling block to the weak and unlearned.
Jesus affirmed that the early chapters of Genesis were historical and factual. Remember that our information on Adam and Eve, and the fall of the human race are contained in these "allegorical" and "morality play" chapters. This is why evangelicals believe these chapters are historical, not a defensive reaction to Darwin.
Since Collins' method emanates from a base that is not constrained by a high view of scripture, his method is faulty. Therefore, we must be very careful about accepting his views based on that method.
Contrast his view of scripture with his view of science:
"Science is progressive and self-correcting: no significantly erroneous conclusions or false hypotheses can be sustained for long, as newer observations will ultimately knock down incorrect constructs."12
I think Collins' faith in science is extreme and unwarranted. Critics of scientism like Kuhn have demonstrated multiple cases where exactly what Collins thinks could never happen has happened (see his The Structure of Scientific Revolutions). Collins' faith in science contrasts strongly with his lack of confidence in scripture, and calls further in to question his underlying assumptions and methods.
Collins on Intelligent Design
Collins' assumption that scientists would never ignore or marginalize a new view, just because it's based on theistic assumptions seems quite naïve to me. Why would scientists be any different than other humans? While they may like formulating new theories, adopting a position that would lead to their own marginalization is not likely.
Collins disqualifies ID as science because "A viable scientific theory predicts other findings and suggests approaches for further experimental verification." But "ID's proposal of the intervention of supernatural forces to account for complex multi-component biological entities is a scientific dead end. Outside of the development of a time machine, verification of the ID theory seems profoundly unlikely."13 I think this criticism fails for more than one reason.
First, macroevolution (as I have defined it above) suffers the same criticism as ID. It prescribes no future approach for experimental verification. Experimental verification of natural selection or of genetic mutation is not the same as verification for macroevolution. Faith in macroevolution rests entirely on interpretation of existing data and has never been validated experimentally, or observed.
Second, while we would have to go back in a time machine to verify ID, we would also need one to validate macroevolution. Collins fails to see that believing in a process that has immense gaps in the fossil record, and no explanation for how it began in the first place is no better than believing in a far more plausible explanation, such as intervention by a designer.
I thought his call for ID to give a mechanism for how the intelligence gets into the design was unrealistic.14 This would be nothing but speculation at best. Any number of possibilities could be suggested, but these would probably only be used to ridicule the position. ID is primarily a critique of a pure Darwinian explanation for nature. Collins seems to imply that ID is in the same category as young earthers, but most are in fact Darwinists within limits. The material I have seen is arguing that Darwin's theory is inadequate to explain all transitions. Most do not deny Darwinian principles across the board.
His arguments that current design in humans is imperfect and flawed, thus making it unlikely they come from God, are very familiar arguments found in enlightenment writings – Darwin, Hume, and others advanced these same arguments, and they have been answered satisfactorily.15 I was surprised to see a theist using these well-known atheistic arguments.
I thought his rejection of the flagellum argument was unconvincing and rhetorically loaded. He throws in qualifiers like "presumably" such and so could have happened, and admits "we are far from filling in the whole picture (if we ever can)," but on these bases, he concludes "Recent research has fundamentally undercut this [ID] position."16 The research he mentions did nothing more than suggest a highly speculative possibility without observable backing [that flagella could have been borrowed toxin injectors somehow converted to a completely different function]. How does this fundamentally undercut anything? I thought it highly questionable that an organelle used to inject toxin into other bacteria would spontaneously begin to spin as a means of motility, and thereafter be reproduced for that purpose. I'm sure Behe et al. would point out that this transition would have to happen for all parts of the flagellum in a very short time in order to bestow any enhanced survivability. I can't believe Collins thinks the matter is closed based on this speculation.
I have never felt that the flagellum and related arguments were the most persuasive part of ID (their work on inorganic evolution is far more convincing, since the mechanisms of mutation and selection are not available as an explanation). But I did not feel that mere resemblance to amino acid sequences in a somewhat similar organelle that had a completely different function could be called "fundamentally undercutting" the flagellum argument.
He also characterizes irreducible complexity as the foundation for ID, and that is inaccurate. That is only one argument use by the group, and in my mind, it is one of the least convincing. The recent discovery that bacteria and viruses can adopt and assimilate loose strands of inter-cellular DNA into their own DNA (not mentioned by Collins) could raise problems for this theory as well.17
He completely fails to deal with their much more substantial work in inorganic evolution. This is a critical shortcoming in his critique. He also fails to deal with Dembski's analysis of what constitutes evidence of design in nature.
Collins includes a theological critique centering again on the 'God of the gaps' complaint dealt with earlier, and a specious claim that ID pictures an incompetent God who needs to intervene periodically to "correct" his shortcomings in previous creation. Neither of these was convincing.
The reasons for progressive creation would not need to be correcting errors or deficiencies. Anyone who has added to his garden during successive years understands why the creative work done last year may be supplemented without any suggestion that the previous work was mistaken. The pleasure of creating is reason enough for a creative being to act. For all we know, progressive acts of creation may have been appropriate because conditions were developing on the planet during long intervals that made further advances possible. There could be other reasons. This critique is an interpretation loaded with negative assumptions not based on any evidence. It is also possible that natural selection and mutation are incapable of developing beyond certain inherent limits.
Collins is completely negative about ID. He predicts it is a ship headed for the bottom of the ocean.18 I thought he gave no adequate basis for this caustic assessment. Young people in our church have supplied me with evidence that in recent months, weblogs and other groups discussing science and Christianity have suddenly shifted from favoring ID to declaring it now "disproven," that "it sucks," and "is stupid." I think Collins' very popular book is having a dramatic but unwarranted impact.
Collins' version of theistic evolution should be called deistic evolution. He only allows God a role at the very beginning, setting up the machine at the time of the big bang. Even the arrival of abstract intelligence, morality, and the desire for God were apparently natural developments.19 God's role is limited to foreknowing that evolution would take this path.20 His position is even more deistic than Darwin's own position, because Darwin said: "Therefore I should infer from analogy that probably all the organic beings which have ever lived upon this earth have descended from one primordial form into which life was first breathed by the Creator."21 Collins won't even allow for God launching the first living cells.
Collins' analysis of why people resist this deistic theory of origins centers on two specious reasons—1) that people don't like theism associated with evolution, and 2) that they prefer controversy to harmony. I can't think of anyone who resists deism for these reasons.
The real reason Christians resist deism is biblical authority and sound exegesis. Here, Collins reveals his method again, in a way consistent with his earlier chapters: Genesis 1 and 2 are figurative. Adam and Eve were not the only humans, because of Cain's wife. Therefore they are probably just a representative story of how people don't obey God. C.S. Lewis and the Pope agree that the passages should not be taken literally or historically. The lyrical character puts them in the same category as Job and Jonah, which do not carry a "historical ring."22
As noted earlier, these verdicts fly in the face of Jesus' clear teaching that "God said" the things recorded in Gen 2 to Adam. Jesus likened his resurrection to Jonah's expulsion by the fish. According to this reasoning, if the Jonah story was mythical, Jesus' resurrection could be mythical also. Paul teaches that just as sin entered through one man, justification entered through one man. Again, if Adam's fall was mythical, wouldn't this mean that Jesus' death and resurrection could be the same? How did the fallen nature pass to other humans? Clearly the Adam and Eve story is impossible if humans evolved in a transitional community of organisms probably comprising thousands of members, as Collins assumes. I hope we all see that viewing humans as the product of evolution alone means the rejection of a literal Adam and Eve. It also offers no adequate explanation for a spiritual nature that would even survive death.
Collins' view of scripture is completely unacceptable.
On page 83, Collins gives us two choices where Genesis interpretation is concerned: hyper-literal young earth hermeneutics, and non-historical poetic license. His coverage in this section demonstrates no understanding of other interpretive positions. Throughout this section, he shows little depth of understanding either of the interpretive issues in Genesis or of the theological issues raised by his low view of scripture.
I would be very concerned if Xenos leaders recommend this book to our people without the strongest warnings. Indeed, I see little reason to recommend the book at all except to advanced believers. We should remember how easily people in Xenos have been led to doubt the early chapters of Genesis in the past. Collins stands close enough to biblical faith to be very appealing, especially because of his preeminence in the scientific community. But while learning from his advanced scholarship in genetics, people could also easily buy into his poorly informed views on scripture.
For us, the determining limits to which theories may be accepted should be biblical exegesis. I believe we have no reason to declare which theory or combination is the correct one, only which theories are possible within a biblical framework.
1. Francis S. Collins, The Language of God, (New York: Free Press, 2006), 93.
2. Francis S. Collins, The Language of God, 93.
3. Francis S. Collins, The Language of God, 95.
4. Francis S. Collins, The Language of God, 94, 95.
5. Carroll, Robert L., "Towards a new evolutionary synthesis," in Trends in Evolution and Ecology 15(1):27-32, 2000, p. 27.
6. Francis S. Collins, The Language of God, 134.
7. Francis S. Collins, The Language of God, 134, 135.
7b. See recent articles such as:
- Now: The Rest of the Genome, New York Times, November 11, 2008.
- "Agency for Science", Technology and Research (A*STAR), Singapore.
- 'Junk' DNA Proves Functional; Helps Explain Human Differences From Other Species, ScienceDaily, November 5, 2008.
8. Francis S. Collins, The Language of God, 175.
9. Francis S. Collins, The Language of God, 175.
10. Francis S. Collins, The Language of God, 175.
12. Francis S. Collins, The Language of God, 58
13. Francis S. Collins, The Language of God, 187.
14. Francis S. Collins, The Language of God, 187, 188
15. Gleason Archer, Survey of Old Testament Introduction, (Chicago: Moody Press, 1974) on Genesis.
16. Francis S. Collins, The Language of God, 192
17. Laurie Garrett, The Coming Plague: Newly Emerging Diseases In a World Out of Balance, (New York, Farrar, Straus and Giroux, 1994)
18. Francis S. Collins, The Language of God, 195.
19. Francis S. Collins, The Language of God, 201. Although he allows that these defy explanation through evolution, he still resists attributing them to God, and maintains that no intervention by God was necessary. He reaffirms this when he describes moral law and desire to know God as gradual, natural developments that could have happened in reptiles if things had gone differently.
20. Francis S. Collins, The Language of God, 205, 207
21. Cited in Gleason Archer, Survey of Old Testament Introduction, 195.
22. Francis S. Collins, The Language of God, 209.
I'm not sure you're interpreting Collins' book in the way he intended it to be understood. I read the book and I got a different impression.
The scarcity of transitions between species isn't because the world magically stopped making fossils and started again; it's because fossilization is rare. The current theory is that a new species will develop in a small area among a limited population and will be rare until it becomes established and begins to spread.
Since the average life time of a species is about 5 million years and the time to develop a new species in in the thousands of years, it would be very difficult for enough animals to become fossilized for scientists to stumble upon the specific location and age of rock that might show a fossil in time to collect it before it weathers away. We have plenty of transitions between orders and families, a few between genera and only a handful between species.
As for animals reproducing after their kind: That's one of the principles of evolution. A bacteria will spawn other bacteria and an archaea will spawn other archaea.
If a bacteria-like blue green algae invades an archaea and establishes a symbiotic relationship, it will reproduce when the archaea does, producing more of its kind, while feeding the archaea on the byproducts of its photosynthesis.Over time the independent functions of each will decay as they aren't needed and they'll become primitive eukaryotic plant cells. The same thing will happen with other bacteria that invade archaea and become mitochondria.
Each generation will be much like their parents as your children are much like you, and each generation will be slightly different as your children are.
And those changes will add up over time: features developing until one generation of semi-long tailed microbes become recognizable as choanoflagelates, and eventually choanoflagelates that develop the ability to make stable colonies might order those colonies into sponges.
That's all evolution is. A slow accumulation of changes.