Well done. Nicely researched book on the DNA evidence for evolution. Particularly liked the explanation of the development of the eye ( )

I think my background is skewing how I see this book. I have an undergraduate degree in biochemistry and a graduate degree in cell, molecular, and developmental biology, so some of the information presented here seemed either oversimplified or obvious. I also have a legal background, and in one of my two constitutional law classes we spent a decent amount of time on the Religion Clauses of the First Amendment. In particular, we learned a great deal about the intelligent design movement and the Kitzmiller v. Dover case, which is discussed (although not by name) in Chapter 9, and I would have enjoyed an expanded discussion of both the case and “irreducible complexity.” Incidentally, Michael Behe and irreducible complexity both showed up in Kitzmiller. Finally, while I accept the theory of evolution - and for people who want to plead "it's only a theory" I also accept the theory of gravitation, the theory of relativity, and the germ theory of disease - and an old earth, I know several young-earth creationists very well and interact with them regularly. With all that in mind, here goes…

First, I appreciated the sections on the mathematics behind evolution, particularly the frequency of new mutations for natural selection to act on. This section would be especially useful when interacting with young-earth creationists, because from what I can see there is a strong belief that the idea of an old earth was postulated primarily because of the time frames required for evolution, so it was useful to see the evidence of the frequency of mutations clearly laid out. And it doesn’t take nearly as long as one might think. Yes, you’d need longer than six thousand years, but four and a half billion years is far more than enough. So, if you have to interact with young-earth creationists and they keep trying to start arguments based on statistics and probability with you, I would recommend reading this book just to get a feel for the numbers. I would not recommend giving it to them; most of them would never read a book with a title like this. However, if you read it yourself you can start bringing up math as soon as they do. One caveat about this chapter: The calculations for mutation frequency don’t explicitly include a calculation for the probability that the mutation will end up in the germ line, and thus be evolutionarily relevant.

As a graduate student, I worked with two highly conserved (“immortal”) gene sequences, including the 16S sequence, so Woese and his work were familiar to me. But I do believe some more explanation should have been included here. While Woese’s work was discussed, the 16S sequence was never brought up by name or even described. I think the 16S gene should have been named and its function described, and then it would have been obvious why this gene is “immortal” and the reasons Woese selected it would have been more clear. Similarly, a conserved region of the elongation factor 1-alpha gene was shown, but there was no discussion of what elongation factor 1-alpha does or why it’s important to cells across all three domains. To me this was a recurring problem; the “why’s” that would have helped the argument were left undiscussed. The preface made it clear this was supposed to be an argument, or a “brief,” in favor of evolutionary theory, and it’s always best to discuss all the relevant information, the reasons why you cited that information, and how it helps the case you’re building. Of course, it’s also best to have a concise argument with a chain of reasoning that can be clearly linked to the “clincher” statement, which were also things I couldn’t always find. Incidentally, there are plenty of highly conserved genes to choose from for a discussion like this, and I think “The Violinist’s Thumb” did a much better job with explaining the conservation of the hox genes.

Because this topic came up in the same chapter, I’ll add that I’d like to learn more about the idea of eukaryotes being the result of a “merger” between bacterial and archaean parents – this version of the tree of life was never presented, even in grad school, and I’m most familiar with the version that has bacteria and archaea splitting off and then eukaryotes splitting off from archaea. Genetic similarities in eukaryotes and archaeans are in genes that encode for enzymes associated with transcription and translation. But eukaryotes have much more in common with bacteria when it comes to genes that encode for enzymes associated with metabolic enzymes or for basic cellular components. The merger idea makes more sense, but if it were widely accepted one would think I’d have heard of it before (the book was published in 2006, when I was in grad school). In addition, the table on page 77 is making me wonder whether there is an upper limit on the number of genes in a genome; if so, it would explain why alternative splicing came to be, even though it is very costly in terms of energy.

Speaking of energetic costs, another thing that drove me crazy is that a discussion of energy requirements when it comes to producing certain proteins was not included. Proteins that might otherwise confer a selective advantage can be so energetically costly to make that they fall out of the pool if the advantage is not immediately apparent. Venoms or poisons tend to be biochemically expensive, and this is one of the reasons why mimicry is such a popular tactic. Similarly, heat-resistant proteins and other cellular components tend to be very costly in terms of energy, so any advantage conferred would need to show up relatively early. In addition, it takes longer and costs more energy to transcribe a larger genome, and so reproduction also takes longer and costs more. These balancing factors were not discussed, and I felt like they should have been.

Furthermore, I’m not even sure who the intended audience for the book is supposed to be. For one thing, while the 16S gene was alluded to but never named and elongation factor 1-alpha was named but never discussed, it seemed like the book was initially targeted toward readers with a casual interest in biology. But then the book brought up specific codons and included portions of protein sequences that were written using the single-letter abbreviations for each amino acid. Although I still remember a lot of biochemistry, I do not remember every single codon or the single-letter abbreviations for each amino acid, and a reader with a more casual interest would likely find it even more confusing. This problem could have been easily resolved by including an appendix with a few tables containing this information. But other parts of the book were obviously geared more towards non-specialists, such as the discussion of opsins. It’s possible to successfully achieve an “in-between” effect, but it’s very rare and usually requires including a lot of technical information somewhere in the book (usually a few appendices) and making it clear that the reader can consult those appendices for a more detailed discussion. This worked well for [b:A Fish Caught in Time: The Search for the Coelacanth|539138|A Fish Caught in Time The Search for the Coelacanth|Samantha Weinberg|https://images.gr-assets.com/books/1347796537s/539138.jpg|1330560].

For the interested (review continues beneath second table):

The codons:



The single-letter amino acid abbreviations:



As for seeking to convince creationists by pointing out the evidence for evolution from molecular biology, I will simply point out that most creationists do not completely discount the idea that both natural selection and evolution can happen. When confronted with the development and spread of antibiotic resistance in bacteria, or the pigment shifts in the peppered moth, they will say these are examples of “microevolution” and this is not the problem. It is “macroevolution” that they object to, and as far as I’ve been able to tell no amount of discussion will convince them that small changes over time can add up to very large changes. Also, pointing out the universally conserved sequences isn’t going to help much at all, because the similarities will be interpreted as evidence for design (think “we create similar tools for similar tasks.”) Under these circumstances, even very strong evidence isn’t going to help nearly as much as one might think.

I did like Chapter 9, and I found the discussion of the most common arguments and tactics used to attempt to undermine scientific arguments interesting, especially because the same pattern is emerging when it comes to climate change in the United States:

1. Doubt the science (and make teaching it effectively impossible)
2. Question the motives and integrity of scientists (and bring up grant funding at every opportunity)
3. Play up legitimate disagreements among scientists, and cite gadflies as authorities (bonus points if you can find credentialed scientists outside the relevant field to take your side – creationists arguing against evolution have been known to cite arguments from “PhD scientists” whose degrees are in physics and astronomy)
4. Exaggerate potential harm
5. Appeal to personal freedom (an especially powerful tactic in the United States)
6. Argue that accepting the science means rejecting the core of another set of beliefs vital to a person, his or her community, or both (bonus points if this is religious faith or political values, which can then be linked to personal freedom)

And I don't think it's a coincidence that the same group of people who oppose the idea of evolution also oppose the idea of climate change. ( )

I think my background is skewing how I see this book. I have an undergraduate degree in biochemistry and a graduate degree in cell, molecular, and developmental biology, so some of the information presented here seemed either oversimplified or obvious. I also have a legal background, and in one of my two constitutional law classes we spent a decent amount of time on the Religion Clauses of the First Amendment. In particular, we learned a great deal about the intelligent design movement and the Kitzmiller v. Dover case, which is discussed (although not by name) in Chapter 9, and I would have enjoyed an expanded discussion of both the case and “irreducible complexity.” Incidentally, Michael Behe and irreducible complexity both showed up in Kitzmiller. Finally, while I accept the theory of evolution - and for people who want to plead "it's only a theory" I also accept the theory of gravitation, the theory of relativity, and the germ theory of disease - and an old earth, I know several young-earth creationists very well and interact with them regularly. With all that in mind, here goes…

First, I appreciated the sections on the mathematics behind evolution, particularly the frequency of new mutations for natural selection to act on. This section would be especially useful when interacting with young-earth creationists, because from what I can see there is a strong belief that the idea of an old earth was postulated primarily because of the time frames required for evolution, so it was useful to see the evidence of the frequency of mutations clearly laid out. And it doesn’t take nearly as long as one might think. Yes, you’d need longer than six thousand years, but four and a half billion years is far more than enough. So, if you have to interact with young-earth creationists and they keep trying to start arguments based on statistics and probability with you, I would recommend reading this book just to get a feel for the numbers. I would not recommend giving it to them; most of them would never read a book with a title like this. However, if you read it yourself you can start bringing up math as soon as they do. One caveat about this chapter: The calculations for mutation frequency don’t explicitly include a calculation for the probability that the mutation will end up in the germ line, and thus be evolutionarily relevant.

As a graduate student, I worked with two highly conserved (“immortal”) gene sequences, including the 16S sequence, so Woese and his work were familiar to me. But I do believe some more explanation should have been included here. While Woese’s work was discussed, the 16S sequence was never brought up by name or even described. I think the 16S gene should have been named and its function described, and then it would have been obvious why this gene is “immortal” and the reasons Woese selected it would have been more clear. Similarly, a conserved region of the elongation factor 1-alpha gene was shown, but there was no discussion of what elongation factor 1-alpha does or why it’s important to cells across all three domains. To me this was a recurring problem; the “why’s” that would have helped the argument were left undiscussed. The preface made it clear this was supposed to be an argument, or a “brief,” in favor of evolutionary theory, and it’s always best to discuss all the relevant information, the reasons why you cited that information, and how it helps the case you’re building. Of course, it’s also best to have a concise argument with a chain of reasoning that can be clearly linked to the “clincher” statement, which were also things I couldn’t always find. Incidentally, there are plenty of highly conserved genes to choose from for a discussion like this, and I think “The Violinist’s Thumb” did a much better job with explaining the conservation of the hox genes.

Because this topic came up in the same chapter, I’ll add that I’d like to learn more about the idea of eukaryotes being the result of a “merger” between bacterial and archaean parents – this version of the tree of life was never presented, even in grad school, and I’m most familiar with the version that has bacteria and archaea splitting off and then eukaryotes splitting off from archaea. Genetic similarities in eukaryotes and archaeans are in genes that encode for enzymes associated with transcription and translation. But eukaryotes have much more in common with bacteria when it comes to genes that encode for enzymes associated with metabolic enzymes or for basic cellular components. The merger idea makes more sense, but if it were widely accepted one would think I’d have heard of it before (the book was published in 2006, when I was in grad school). In addition, the table on page 77 is making me wonder whether there is an upper limit on the number of genes in a genome; if so, it would explain why alternative splicing came to be, even though it is very costly in terms of energy.

Speaking of energetic costs, another thing that drove me crazy is that a discussion of energy requirements when it comes to producing certain proteins was not included. Proteins that might otherwise confer a selective advantage can be so energetically costly to make that they fall out of the pool if the advantage is not immediately apparent. Venoms or poisons tend to be biochemically expensive, and this is one of the reasons why mimicry is such a popular tactic. Similarly, heat-resistant proteins and other cellular components tend to be very costly in terms of energy, so any advantage conferred would need to show up relatively early. In addition, it takes longer and costs more energy to transcribe a larger genome, and so reproduction also takes longer and costs more. These balancing factors were not discussed, and I felt like they should have been.

Furthermore, I’m not even sure who the intended audience for the book is supposed to be. For one thing, while the 16S gene was alluded to but never named and elongation factor 1-alpha was named but never discussed, it seemed like the book was initially targeted toward readers with a casual interest in biology. But then the book brought up specific codons and included portions of protein sequences that were written using the single-letter abbreviations for each amino acid. Although I still remember a lot of biochemistry, I do not remember every single codon or the single-letter abbreviations for each amino acid, and a reader with a more casual interest would likely find it even more confusing. This problem could have been easily resolved by including an appendix with a few tables containing this information. But other parts of the book were obviously geared more towards non-specialists, such as the discussion of opsins. It’s possible to successfully achieve an “in-between” effect, but it’s very rare and usually requires including a lot of technical information somewhere in the book (usually a few appendices) and making it clear that the reader can consult those appendices for a more detailed discussion. This worked well for [b:A Fish Caught in Time: The Search for the Coelacanth|539138|A Fish Caught in Time The Search for the Coelacanth|Samantha Weinberg|https://images.gr-assets.com/books/1347796537s/539138.jpg|1330560].

For the interested (review continues beneath second table):

The codons:



The single-letter amino acid abbreviations:



As for seeking to convince creationists by pointing out the evidence for evolution from molecular biology, I will simply point out that most creationists do not completely discount the idea that both natural selection and evolution can happen. When confronted with the development and spread of antibiotic resistance in bacteria, or the pigment shifts in the peppered moth, they will say these are examples of “microevolution” and this is not the problem. It is “macroevolution” that they object to, and as far as I’ve been able to tell no amount of discussion will convince them that small changes over time can add up to very large changes. Also, pointing out the universally conserved sequences isn’t going to help much at all, because the similarities will be interpreted as evidence for design (think “we create similar tools for similar tasks.”) Under these circumstances, even very strong evidence isn’t going to help nearly as much as one might think.

I did like Chapter 9, and I found the discussion of the most common arguments and tactics used to attempt to undermine scientific arguments interesting, especially because the same pattern is emerging when it comes to climate change in the United States:

1. Doubt the science (and make teaching it effectively impossible)
2. Question the motives and integrity of scientists (and bring up grant funding at every opportunity)
3. Play up legitimate disagreements among scientists, and cite gadflies as authorities (bonus points if you can find credentialed scientists outside the relevant field to take your side – creationists arguing against evolution have been known to cite arguments from “PhD scientists” whose degrees are in physics and astronomy)
4. Exaggerate potential harm
5. Appeal to personal freedom (an especially powerful tactic in the United States)
6. Argue that accepting the science means rejecting the core of another set of beliefs vital to a person, his or her community, or both (bonus points if this is religious faith or political values, which can then be linked to personal freedom)

And I don't think it's a coincidence that the same group of people who oppose the idea of evolution also oppose the idea of climate change. ( )

Carroll starts out by talking about forensic use of DNA evidence in criminal cases, where we rely on DNA evidence to determine guilt or innocence, often in cases where the death penalty or long imprisonment is at stake. He explains, in simple terms, how this works and why it matters.

And then he explains the contradiction between the wide popular acceptance of DNA evidence by the general public, and the widespread resistance to or rejection of evolution.

Organized in three main sections, Carroll lays out, first, how DNA analysis works, why it is solid evidence of evolution, and how it enables us to decipher the evolutionary history of organisms; what it tells us about how evolution has worked, focusing on specific examples such as the evolution of vision in insects, primates, cetaceans, and fish, and why Antarctic ice fish have no hemoglobin in their blood; and finally, the major arguments against evolution and responses to them.

The book is written in clear, understandable terms. Carroll acknowledges that some of the concepts are complex, but says they're both important and within the ability of the reader to understand, and then proceeds to explain them in an accessible way without talking down to his readers. In the audio version, we don't get the benefit of seeing the figures and illustrations while listening to the text, but in the audio CD edition, they are included on the final disk. In the final section, refuting objections to evolution, Carroll is respectful and never mocks those he disagrees with, but is absolutely firm and clear about why they are wrong.

Patrick Lawlor, as the reader, is excellent, with a clear, expressive voice that captures, I think, exactly the tone that Sean Carroll intended.

Highly recommended.

I borrowed this book from a friend. ( )

It's a very rare book review that causes me to immediately go and purchase a book. But that's exactly what I did when I stumbled across a glowing review while browsing SEED's science blogs. Clearly I was feeling a serious lack of science and critical thinking in my life that day.

While I have some criticisms of this book, most of them stem from the fact that it was written for a general audience (and I'm glad that it was) and so sometimes had less detailed descriptions of physiology than I would have liked to see. But I'm getting ahead of myself! The Making of the Fittest examines DNA evidence as the ultimate forensic proof of evolution -- rightly pointing out that DNA evidence is routinely used and universally accepted in courts of law. Which raises the question -- how can someone accept, say, the use of DNA to prove paternity, and yet not accept the overwhelming evidence provided by DNA analysis as to the mechanisms and effectiveness of evolution?

Carroll takes a comprehensive approach to proving his case -- from addressing common arguments of evolution-deniers (most notably that evolution "couldn't have had enough time" and the evolution of the human eye), showing examples both of useful genes deteriorating when selection pressure was removed and of how under similar selective pressures, many species independently evolved the same adaptations, to some interesting discussions of other historical resistances to other scientific ideas, and why this resistance happens over and over with major new ideas.

I really enjoyed this book and would recommend it to anyone interested in evolution. ( )