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Friday, October 31, 2014

99%? 95%? 87%? 70%? How Similar is the Human Genome to the Chimpanzee Genome?

Posted by jlwile on March 18, 2010

I recently got an E-MAIL from a student who heard a “university professor” say that the human and chimpanzee DNA are 99% similar. She asked whether or not the professor was correct and, if not, how similar is human DNA to chimpanzee DNA?

Well, the answer to her first question is quite easy. The professor was horribly wrong. The nonsensical idea that human and chimp DNA are 99% similar comes from misinterpreting a 1975 paper by Mary-Claire King and A. C. Wilson. 1 This groundbreaking (for its time) article compared several proteins in chimpanzees to their equivalent proteins in humans.

In case you don’t know, proteins are complex molecules that are composed of many smaller molecules (called amino acids) linked together. The primary structure of a protein is simply the order in which its amino acids link up. King and Wilson showed that in many, many proteins, the difference in the primary structures of chimpanzee and human proteins was about 1%. Since DNA determines the order of amino acids in each protein an organism makes for itself, they made the reasonable inference that for the portions of DNA that code for those proteins humans and chimpanzees are 99% similar.

However, the genes that code for these proteins make up a tiny, tiny fraction of the human or chimp genome, and only SOME of those proteins were studied. Thus, the idea that one can extend that number to the entire genome and say that human and chimp DNA are 99% similar is just absurd.

As time went on, of course, we started being able to directly analyze the DNA of an organism and directly compare one genome to another. DNA has several components, but the information-coding part of DNA is composed of nucleotide bases that come in one of four forms: adenine (A), thymine (T), cytosine (C), and guanine (G). These bases link together to hold the DNA in its familiar double-helix structure. However, C can link only to G (or vice-versa) and A can link only to T (or vice-versa). Two nucleotide bases linked together are called a “base pair,” and the order of its base pairs is the way DNA codes its information.

In 2002, a study analyzed roughly 1 million base pairs of the human genome and the chimp genome, and it found that those sections of DNA were about 95% similar.2 Given that there are roughly 3.2 billion base pairs in the human genome, it is clear that such a comparison, while better than that done by King and Wilson, is still such a tiny sample that you really can’t reasonably say anything about how the human and chimp genomes compare.

In 2003, another study looked at 1.9 million base pairs on another part of the chimp and human genome, and it found only 87% similarity. 3 Once again, compared to the total size of the genome, this is a pretty small chunk.

Then things became a lot clearer…sort of. In 2005, the complete draft sequence of the chimpanzee genome was published.4 As a result, the entire chimpanzee genome could be compared to the entire human genome. What was learned? Well, that depends on exactly how things are compared.

The most logical way to compare two genomes is to find the parts that match nearly perfectly. When that is done, we find that 2.4 billion of the base pairs of the human genome line up “nearly” perfectly with 2.4 billion of the base pairs of the chimp genome. As the 2005 paper on the draft sequence says:

Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover 2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y. 5

So, out of the 3.2 billion base pairs in the human genome (and about the same in the chimp genome), 2.4 billion of them line up nearly perfectly. It turns out that there are some differences within these 2.4 billion base pairs, and they account for about 3% of those 2.4 billion base pairs.

So…if those 2.4 billion base pairs lined up perfectly, the chimp and human genome would be about 75% similar. However, given that 3% of those base pairs don’t line up perfectly, human and chimp DNA are about 72% similar. Several geneticists have obviously looked at these data, and there are those who think the number will eventually drop below 72% once all the data are in. In fact, Dr. Richard Buggs (geneticist at the University of Florida) says

I predict that when we have a reliable, complete chimpanzee genome, the overall similarity of the human genome will prove to be close to 70% (and very far from 99%).6

In spite of what the data say, PBS asserts the following:

Today, many a schoolchild can cite the figure perhaps most often called forth in support of [a common ancestor for apes and humans]—namely, that we share almost 99 percent of our DNA with our closest living relative, the chimpanzee. 7

I think PBS needs to stop listening to schoolchildren when it comes to evidence for evolution. Of course, the big question is: If 99% similarity was such strong evidence for a common ancestor between chimpanzees and humans, will 70% similarity be considered evidence against a common ancestor? Of course not! Evolution can use special pleading to accommodate any data. It does so with the fossil record, homology, etc. Why not do it with genome similarities as well?

REFERENCES

1. Mary-Claire King and A. C. Wilson, “Evolution at Two Levels in Humans and Chimpanzees,” Science 188:107-16, 1975
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2. Brittin, R., “Divergence between Samples of Chimpanzee and Human DNA Sequences is 5%, Counting Indels,” Proceedings of the National Academy of Sciences, USA 99:13633-35, 2002
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3. Tatsuya, A., et al. , “Comparative Sequencing of Human and Chimpanzee MHC Class I Regions Unveils Insertions/Deletions As the Major Path to Genomic Divergence,” PNAS USA 100:7708-13, 2003
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4. The Chimpanzee Sequencing and Analysis Consortium, “Initial sequence of the chimpanzee genome and comparison with the human genome,” Nature 437:69-87, 2005
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5. Ibid, p 71
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6. http://www.refdag.nl/artikel/1378077/70+Chimp.html
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7. http://www.pbs.org/wgbh/nova/id/pred-nf.html
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Comments

25 Responses to “99%? 95%? 87%? 70%? How Similar is the Human Genome to the Chimpanzee Genome?”
  1. Little Jimmy says:

    Dr. Wile,

    I just found your blog and I love it! I have read through almost all of your posts. I especially enjoyed your documentation of the data regarding global warming. I have a question, and this seemed like an okay place to raise it.

    Scripture (at least as I have always understood it) teaches that man and animals are different kinds of beings. Man is uniquely in the image of God and given dominion over all other animals, etc.

    But the observations of science tend to make it look like the difference between man and the higher primates is only one of degree. After all, chimps have advanced thinking and communication skills (I am thinking especially of those that have been taught to communicate with humans in various froms). Their central nervous system’s are (relatively) similar to ours, etc. They just seem to be a little lower on the scale.

    How do you deal with this tension?

    LJ

  2. Let me build off of Little Jimmy’s question, which is quite good. How does Creation Science explain why 70% of the human and chimpanzee genomes are the same?

  3. jlwile says:

    LJ, thanks for the comment and the kind words. I think you are confusing biological functionality with what makes a person a person. Humans have a lot of biology in common with primates. They have less (but still a lot of) biology in common with other mammals. They have even less (but still a lot of) biology in common with non-mammal vertebrates. However, this all makes perfect sense. After all, from a functional view, we are very similar to these creatures. For example, humans and nonhuman primates have very similar vision (human vision being a bit superior) and very similar senses of smell (nonhuman primates typically being slightly superior). Thus, it is not surprising that we have similar biological structures and genes related to those senses. All mammals are warm-blooded. Thus, it is not surprising that we have similar biological structures and genes when it comes to metabolism and circulation. All vertebrates have backbones. Thus, it is not surprising that we have similar biological structures and genes when it comes to the skeletal system. However, these are all simply FUNCTIONAL things – things that keep us alive. They simply show that the functions of life are the result of a common designer.

    When it comes to the things that make a person a person, we are clearly unique. We can learn things and pass them down to the next generation, which can build on those learned things and learn even more. We can think about things like ethics and morals. We can create things that make life better (or worse) for all humankind. These are all uniquely human characteristics that make us clearly distinct from the rest of Creation. In short, we can do more than just survive, because we are completely different. Of course, to do more than survive, we first must survive. Thus, our biological structures related to survival are sometimes quite similar to those of the animals, as they must also survive.

    One thing I might also point out is that while chimps clearly are smart (for animals), they are not unique in this regard nor demonstrably superior to other smart animals. For example, chimps can use tools to solve problems and modify them to some extent, but crows can do exactly the same thing. In fact, there are some scientists who consider crows to be smarter than chimpanzees. Dolphins are regarded by some scientists as second only to humans in intelligence. They also use tools in the wild. It is common for people to look at chimpanzees through an evolutionary lens and claim that they are so smart because they are supposedly so closely related to humans. However, other animals that no evolutionist would claim are closely related to humans match or exceed chimpanzee intelligence.

  4. jlwile says:

    Shooter, creation science predicts a lot of similar genes between all organisms in Creation, as they were all made by the same Designer. It also predicts that organisms with similar biological needs will have even more similar genes, as a good Designer often modifies a standard design to solve new problems. Just as all Chevrolets have some things in common, all organisms have some things in common, as they are the result of common Design. Just as a Chevy Camaro has more in common with a Chevy Corvette than it does with a Chevy Colorado, organisms that fill similar ecological niches will be more similar than those that fill different ecological niches. This argument applies to the genomes as well.

    At the same time, creation science predicts that while similar creatures will have similar genes, there is an inherent limit to the flexibility of the genome. Thus, there will be significant genomic gaps between the created kinds.

  5. “I think you are confusing biological functionality with what makes a person a person.” What’s the difference? Aren’t they both based on DNA?

    “Humans have a lot of biology in common with primates. They have less (but still a lot of) biology in common with other mammals. They have even less (but still a lot of) biology in common with non-mammal vertebrates.” Darwinian evolution says this is because they all share a common ancestor. More similar animals have more recent common ancestors. What is creation science’s reason why this is?

    “All mammals are warm-blooded” and “all vertebrates have backbones.” These two statements are simply tautologies. They state that mammals have “similar biological structures and genes when it comes to metabolism and circulation.” And vertebrates have “similar biological structures and genes when it comes to the skeletal system.” That is their definition. Again, Darwinian evolution says that all mammals had a common ancestor (which wasn’t necessarily a mammal, by the way), so they share biological functionality. And since all mammals are vertebrates, but not all vertebrates are mammals, the common ancestor of all vertebrates occurred farther back in the past than the common ancestor of all mammals. What is creation science’s answer for why all mammals are warm-blooded? And why all mammals are vertebrates but not all vertebrates are mammals?

    “These are all uniquely human characteristics that make us clearly distinct from the rest of Creation.” But at one time, there were more than one species of hominin alive at the same time. At that time the distinction between the ancestors of humans and the other hominins were much less distinct. As it happens, modern humans out competed all other hominins (they all occupied the same ecological niche), so the other species all went extinct. Leaving us much more distinct from our most similar primate cousin today, the chimpanzee, than existed at one time in the past.

  6. Hey, we’re both online! How ya doing?

    You admit micro-evolution occurs, right? When you can show that Chevys can evolve changes in their structure by themselves, then you can use cars as an example of Design. Until then, stick to biological examples.

    “there is an inherent limit to the flexibility of the genome.” What is that limit? Since one gene can change at a time (one generation), why isn’t the genome perfectly flexible?

    PS Why do you add around 5 to 10 numbers to your post numbering system? This post is numbered 697, but the previous was 694, that previous was 691, that previous was 682, etc. I’d guess you’ve had between 100 and 200 total posts. You’re obviously a prodigious writer, why inflate the numbers?

  7. jlwile says:

    I’m doing great, thanks for asking. How about you?

    “Aren’t they both based on DNA?” To some extent, yes, but not completely. It is hyper-reductionist thinking to assume that everything that makes an organism an organism is based on DNA. Indeed, current research doesn’t support that. Read Marc Kirschner and John Gerhart’s The Plausibility of Life: Resolving Darwin’s Dilemma to learn about this. Of course, the vast differences between the chimpanzee and human genomes (more than imagined by evolutionists) shows that even genetically, chimps and humans are vastly different. Once again, that is very consistent with the predictions of creation science, which says the created kinds should have significant differences genetically.

    “Darwinian evolution says this is because they all share a common ancestor. More similar animals have more recent common ancestors. What is creation science’s reason why this is?” I think you still need to work on your reading. The similarities result from needing similar structures to fill the ecological niches for which they were designed.

    “What is creation science’s answer for why all mammals are warm-blooded?” Keep up, Shooter. They are designed to fill similar ecological niches. Being warm-blooded is necessary to fill certain ecological niches.

    “And why all mammals are vertebrates but not all vertebrates are mammals?” They are designed to fill DIFFERENT ecological niches. A backbone offers definite advantages in many niches, but warm-bloodedness does not offer a definite advantage in all the niches where a backbone offers an advantage. Thus, to balance all ecosystems, there need to be warm-blooded vertebrates and cold-blooded vertebrates.

    “But at one time, there were more than one species of hominin alive at the same time…” Of course that is not true. It is what you WANT to believe, but it is certainly not backed up by the data. The fossil data show that Humans have always been humans and apes have always been apes.

    “When you can show that Chevys can evolve changes in their structure by themselves, then you can use cars as an example of Design. Until then, stick to biological examples.” So Chevys weren’t designed? That’s how far you have to go to continue to use evolutionary thinking. Wow! Of course Chevys were designed, so they are excellent analogies to biological design. Indeed, they can also change as a result of environmental changes, just as biological organisms can. The 2009 Chevy Corvette ZR1, for example, can “adapt to driver inputs and changing conditions of the road virtually instantaneously.” This is all based on the PROGRAMMING of the designer. The limit of its ability to adapt is the limit of the programming. In the same way, the limit of genetic change is the limit of the programming of the Designer. In fact, this is the main subject of Behe’s book, The Edge of Evolution.

    “why isn’t the genome perfectly flexible?” Because it is an information system. No information system is perfectly flexible. Information systems are structured and highly ordered. They can be changed to some extent, but at some point, you reach the limit of the structure and order. Information theory deals with this in great depth.

    “PS Why do you add around 5 to 10 numbers to your post numbering system?…why inflate the numbers.” Boy, you really do jump to conclusions, don’t you? No wonder you are an evolutionist! I have no control over the numbers used to identify the entries. That’s a WordPress function. I just click “Add New” to add a new article. WordPress creates the unique identifier.

  8. Just fine, thanks.

    “Once again, that is very consistent with the predictions of creation science, which says the created kinds should have significant differences genetically.” I know you’re really big on predictions, so what was the specific numerical prediction of creation science as to the similarity of chimp and human genomes before either were mapped? What is the cutoff amount of difference to achieve “significant differences genetically”?

    “The similarities result from needing similar structures to fill the ecological niches for which they were designed.” So all ecological niches have remained unchanged since creation? What about the flood? Are you saying that it didn’t alter any ecological niches?

    You need to update your taxonomy terminology for primates. Hominin is used instead of hominid when referring only to humans and their closest ancestors, genera Homo, Australopithicus, Ardipithecus, Orrorin, etc. but not Pan (chimps) or Gorilla. Just sticking to Homo, I state that of these species of Homo, some were living on earth at the same time:

    Homo sapiens
    Homo erectus
    Homo floresiensis
    Homo habilis
    Homo neanderthalensis
    Homo heidelbergensis
    Homo ergaster

    I further state that H. sapiens had at one time much more closely related cousins, for instance, H. neanerthalensis. However, all other species of Homo went extinct, leaving the closest relative to humans much more different than existed at one time. (I tried reading the AiG page, but when I get to statements like this: “Interpretation of fossils from an evolutionary perspective is not compatible with the teachings of the Bible.” I just can’t take it seriously.)

    I didn’t mean to say Chevy’s weren’t designed, of course they are. I left out “Intelligent” meaning ID theory.

    OMGs, you know nothing about Information Theory if you can write, “They can be changed to some extent, but at some point, you reach the limit of the structure and order.” Just what does that even mean? Besides being useless, the linked article doesn’t mention anything about a “limit of the structure and order.” Is there no end to the branches of science you can mangle?

  9. jlwile says:

    “What was the specific numerical prediction of creation science as to the similarity of chimp and human genomes before either were mapped?” There wasn’t one. However, evolution didn’t predict one either. However, we can say that creationists were closer to the correct answer, given the fact that evolutionists routinely spouted numbers like 99% and 98%, while baraminology predicted a much larger difference.

    “What is the cutoff amount of difference to achieve “significant differences genetically?” We don’t know enough about genetics to know the cuttoff, but once again, since there is a large difference between chimp and human DNA, creationists were clearly more correct than evolutionists.

    “So all ecological niches have remained unchanged since creation? What about the flood? Are you saying that it didn’t alter any ecological niches?” Once again, you need to work on your reading skills. I said that organisms ADAPT to their CHANGING environment. Thus, ecological niches don’t stay the same. They change, and within the limits of their programming, organisms change to adapt.

    If you had bothered to read the AiG page (I know, your unscientific preconceptions don’t let you do that), you would know that the genus Homo is composed only of fully human people. They all have the same uniquely human characteristics. Only evolutionary storytelling makes them less than fully human.

    Of course I know quite a bit about Information Theory. You clearly don’t, if you couldn’t understand my statement. Is there no end to the branches of science you know nothing about? Let me break it down to a lower level for you. A story (I know, you have a hard time reading, but bear with me) is a system of information. You can alter it to some degree (change the beginning, change the ending, add a few details to the plot, etc.), but there is a limit. You can’t just add ANYTHING to the story, or it will stop making sense. For example, you can’t add lots of nonsense words. You also can’t add words from another language. You can’t even add English words that don’t relate to the story. if your story is a non-fiction account of someone’s life in the 17th-century, for example, you can add all sorts of things relevant to that time and the story, but you can’t add a Boeing 747 to it. That’s the limit of the structure of the information. Come on, Shooter, this isn’t that hard. You can learn it if you concentrate!

    Once again, I know you have a rough time reading, but the article on information theory gives you a detailed discussion of information theory and how it applies to biological systems. If you want to stop making ignorant statements about information theory, you should read the article and try to learn from it.

  10. Ben Michael Fournier says:

    There’s not a lot I can say about this issue, but Dr Sarfati had made a clip in regard to it, (the common design versus common ancestry, homology/DNA percentages issue that is,)

    http://www.youtube.com/watch?v=c7lnLCatp64

  11. So, you say God designed animals to fill ecological niches at creation, then those niches changed over time – including a drastic one at the flood event – and animals adapted to these changes within certain limits (kinds?). Is that it?

    Again, you say the genus Homo only includes humans. Were Adam and Eve were the first Homo species? Which species were they? And what are the time ranges the other species lived? Did they overlap in time?

    What about the other hominin genera, such as Australopithicus and Ardipithecus? Were they human? If so, which genus do Adam and Eve belong to? When did these and other hominin genera live?

    You’re still off on Info Theory. A language is a code that makes sense of bits of information. Whether it is understandable (decode-able) is a property of the code, not the underlying information. Charles Seife, a great science writer, explains this very well in Decoding the Universe.

    You can make a weak analogy between language and genetic changes. The information in the DNA base pairs are decoded by the proteins to perform tasks (communication). Certain mutations produce a message that is unintelligible by the proteins, thus interrupting the communication. Some communications are so important that changing them even slightly causes all further communication to cease (the organism does not survive, most likely in developmental mutations).

    However, there is no limit to which base pairs can mutate. The underlying information is completely flexible (beyond the A-T and G-C relationships). Can you tell me one gene that cannot mutate?

  12. jlwile says:

    “So, you say God designed animals to fill ecological niches at creation, then those niches changed over time – including a drastic one at the flood event – and animals adapted to these changes within certain limits (kinds?). Is that it?” Yes

    “Again, you say the genus Homo only includes humans. Were Adam and Eve were the first Homo species? Which species were they? And what are the time ranges the other species lived? Did they overlap in time?” Of course Adam and Eve were the first Homo species. Since we don’t have their fossils, it is hard to say which species they are. However, I would expect that they are different enough from Homo sapiens (and every other Homo species) that they would probably be classified as a different species altogether. Of course the other Homo species overlapped in time.

    “What about the other hominin genera, such as Australopithicus and Ardipithecus? Were they human? If so, which genus do Adam and Eve belong to? When did these and other hominin genera live?” Once again, if your unscientific preconceptions would not keep you from reading serious discussions of science, you would have learned that Australopithicus and Ardipithecus are not human. They are apes. They lived at the same time as humans.

    You are the one who is off on information theory, as your comments clearly show. If you want to actually learn how it relates to evolution, you should read a serious book about it. Of course, since you are afraid to read the other things I posted, I doubt you will actually do that.

    Your ignorance of information theory is best shown by your silly question, “Can you tell me one gene that cannot mutate?” That has nothing to do with the flexibility of the information in DNA. All genes can mutate, but the act of mutation either ADDS NOTHING to the information or DETERIORATES the information. It does not add new information. Thus, the specific information system of DNA is limited by the ORIGINAL AMOUNT of information in it. As even a cursory understanding of information theory tells us, random mutations do not add genetic information. If you think gene duplication would allow information to be added to the genome, you need to learn some basic genetics.

  13. Please tell me creation science’s best guess as to how long ago Adam and Eve lived.

    I am really tired of you citing a creationist source, not quoting any relevant text, telling me to read all of it and assuming your point is made if I don’t. Werner Gitt’s book in online. Cite the relevant section. Btw, here’s a post on gitt’s theories. What specifically does the writer get wrong? And here’s a long post on Gitt’s talk at the 2005 Creation Mega Conference. Point out the places the reviewer was wrong and Gitt was right.

    The Bergman paper contains one mention of the word “information” and it has nothing to do with information theory. Just what did you want to cite from this paper?

  14. Ben Michael Fournier says:

    “Please tell me creation science’s best guess as to how long ago Adam and Eve lived.”

    This wouldn’t be via science, but by historical backtracking/chronology, that Adam would have lived around 6012 to 5082 years ago, plus or minus a couple centuries.

  15. jlwile says:

    “Please tell me creation science’s best guess as to how long ago Adam and Eve lived.” I have answered this question before, so I am not sure why you keep asking it. My interpretation of the data relative to the age of the earth puts it at around 10,000 years. That’s what I would consider a good guess for how long ago Adam and Eve existed.

    I know you are tired of me destroying your arguments with science, but that’s the way it goes.

    The relevant section of Werner Gitt’s book is the entire book, as you clearly know virtually nothing about information theory. Thus, you need to start from the beginning if you want to learn. I doubt that you really want to learn, however.

    Mark C. Chu-Carroll’s discussion of Gitt’s book is filled with mostly nonsense. For example, he honestly tried to compare the information density of diamond to that of DNA? That is sheer nonsense. DNA is a structured information system that codes for specific information. The impurities in a crystal don’t code for ANYTHING. So the information density in a diamond crystal is ZERO. Also, he doesn’t seem to understand that Gitt is writing an INTERPRETATION of Shannon’s information theory. Gitt is using Shannon’s theory as a STARTING point. The author seems to want him to not go beyond Shannon’s theory. That’s not the purpose of the book.

    The first problem with Jason Rosenhouse’s review is that it contains the same unscientific preconceptions that most of your posts do. He admits that he wants to dismiss Gitt as a crank because he doesn’t like Gitt’s conclusions. Ignoring evidence because you don’t like the conclusions is not science. He actually doesn’t refute anything Gitt says. Instead, he just says things like, “There’s a lot to criticize in those “laws” but let’s stay big picture for the moment.” Of course, he never goes back to refute the laws. He also says things like, “Whoa! Stop the presses! Does the information encoded in our genes really possess the properties Gitt requires? Is Gitt really attributing to genes meaning and purpose?” Of course Gitt does, and it makes sense. The author doesn’t like it, but he doesn’t give any indication as to why Gitt is wrong. In fact, like most anti-creationist nonsense, the article is short on substance and long on mocking. I can see why you like it so much.

    Once again, the Bergman paper was given so that you could actually LEARN something about information theory and how it relates to biological systems. It is unfortunate that you don’t have the guts to read it and learn from it.

  16. Lane Lester’s article from Creation Magazine in 1998 is laughable. Is he still the managing editor of Creation Research Society Quarterly? Or is he even still alive today* ? I know he’s not at Emmanuel College anymore. Just how is he highly qualified, anyway? No matter, I’m just curious. To the article:

    “Genetics and evolution have been enemies from the beginning of both concepts.” Does he mean to say they are still enemies? Because the Modern Evolutionary Synthesis depends on them being friends. (btw, see note 1 from this article)

    “At the same time that Darwin was claiming that creatures could change into other creatures, Mendel was showing that even individual characteristics remain constant.”

    ‘Creatures changing into other creatures’ is a common creationist deliberate obfuscation. As his famous title makes clear, Darwin claimed new species could develop from previous ones. That in no way says one creature turns into another. The previous species does not disappear, it remains contemporaneous with the new one. It is only reproductively isolated from the new one (which is one definition of species, btw).

    Mendel did show individual traits can remain constant, although this means the recessive expression does not disappear. However, not only did Mendel’s experiments only reach the wider scientific community until 20 years after both Darwin’s and Mendel’s deaths, but Mendel’s experiments are the classic example of artificial selection of only a handful of generations. His work has no immediate impact on evolutionary theory. It is only through population genetics, which Mendel knew nothing of, does it create the Modern Synthesis.

    “To help us develop a new biology based on creation rather than evolution,” It is refreshing when creationists are up front about their goals.

    “He thus explained the origin of the giraffe’s long neck in part through ‘the inherited effects of the increased use of parts’.” In part, yes. One of two mentions of this phrase in a later edition of the Origin makes clear Darwin didn’t count on it to drive evolution: “We should keep in mind, as I have before insisted, that the inherited effects of the increased use of parts, and perhaps their disuse, will be strengthened by natural selection. For all spontaneous variations in the right direction will thus be preserved; as will those individuals which inherit in the highest degree the effects of the increased and beneficial use of any part. How much to attribute in each particular case to the effects of use, and how much to natural selection, it seems impossible to decide.”

    “But it is limited because virtually all of the variations are produced by a reshuffling of the genes that are already there.” This is true for Mendel’s experiments, which are untouched by genetic mutation, because of the limited number of generations causes any coding gene mutation to be extremely rare, and any mutation to the genes that control the trait being examined are infinitesimal. They are also conducted in a controlled environment, the ecological niche is constant. It does not apply to mutations over thousands of generations that are acted upon by changing environmental conditions.

    “The different species of Galápagos finches have been observed interbreeding at times, clear evidence that they belong to the same created kind.” (note 2) Does he mean the observations were of fertile offspring or just that they “did it”? In the first case, it only shows that the species are not completely reproductively isolated yet (and it’s possible that the isolation will reverse, recombining into one species). In the second case, it is evidence of nothing but strong sexual drive (and some creativity).

    “since 1910 when the first mutation was reported, some 3,000 mutations have been identified.” Note 3 shows that the sentence should end with “up until 1967.” Ask Jerry Coyne if there have been beneficial mutations of fruit flies.

    Gotta run, I’ll be baaaaaack…

    * Or recently deceased.

  17. jlwile says:

    Shooter, your response to Lane Lester’s article is what’s laughable. I have no idea whether he is alive today or not. I have never met him and know little about him. However, he clearly understands evolution and genetics better than you! Genetics and evolution are clearly enemies. Evolution requires that information gets added to the genome. Genetics stubbornly shows that this cannot happen, despite the fervent faith of neo-Darwinists. This is why so many creation scientists on the list you linked have degrees in genetics, including Lester.

    “Creatures changing into other creatures’ is a common creationist deliberate obfuscation” is a common evolutionist obfuscation. This doesn’t imply that the original creatures dies out. It means exactly what it says – evolution requires one creature to evolve into another.

    Probably the most nonsensical thing you said in your comment is, “Mendel’s experiments are the classic example of artificial selection of only a handful of generations. His work has no immediate impact on evolutionary theory.” First, if you would actually read Darwin’s book, you would see that he spends a LOT of pages arguing that artificial selection provided great evidence for natural selection. Second, Mendel’s work clearly does have immediate impact on evolutionary theory, as it tells us that for a new phenotype to emerge, new alleles must be formed. In other words, information has to be added to the genome – something genetics tells us doesn’t happen.

    Remember what the famous inventor of the gene gun (J.C. Sanford) said, “For several decades, this was the main thrust of crop improvement research. Vast numbers of mutants were produced and screened, collectively representing many billions of mutation events…The effort for the most part was an enormous failure…low phytate corn is the most notable example of successful mutation breeding…The low phytate corn was created by mutatagenizing corn, and then selecting for strains wherein the genetic machinery which directs phytic acid production had been damaged.” [J.C. Sanford, Genetic Entropy & The Mystery of the Human Genome, p. 25, 2005]

    You might have faith enough to believe against what the data say, but I do not.

    “Does he mean the observations were of fertile offspring or just that they “did it”?” He means they produced offspring. If you would actually spend some time learning about these things, you would find that there have been many, many documented cases. For example, Jonathan Weiner, in his 1995 book The Beak of the Finch reports about a case of interbreeding between Geospiza scandens and G. fortis that produced four offspring. Those offspring produced 45 offspring, and THOSE offspring produced more offspring. This, of course, shows that they both have very similar genomes, indicating they are part of the same created kind. Lester is correct, you are not.

    I’ll be here, ready to correct all your mistakes, as usual.

  18. Call me stupid – no wait, you already have – but I don’t understand what you mean when you keep prattling on about adding information to the genome: “Evolution requires that information gets added to the genome. Genetics stubbornly shows that this cannot happen.” Evolution requires information in a genome to change (mutations), but how is that an addition? Are you saying genetics denies mutation?

    “This is why so many creation scientists on the list you linked have degrees in genetics.” The list has 10 geneticists, that’s so many? How about the reverse, how many geneticists are creation scientists? 1%? .01%? .001%? .0001%?

    “Evolution requires one creature to evolve into another.” A common creationist argument against evolution is, “if we’re descended from monkeys, why are there still monkeys?” So it’s best to be clear about this. One into another, your words for the evolutionist position, implies that the original one is longer in existence. That is not the evolutionist position. One sub-population of a species gets reproductively isolated from the main population (sexual selection or geographic distribution are two mechanisms), thus a new species is originated. I try to accurately describe your positions, I would appreciate the same from you.

    As for Mendel, one point was the relatively few generations of plants he studied. But you are right, I shouldn’t have called Mendel’s work artificial selection, that was sloppy. Mendel mated all possible combinations of offspring each generation to see what the results would be. It was not artificial selection. Darwin’s examples of artificial selection were all over many generations and involved the breeders selecting a certain trait, and only breeding individuals with strong expressions of the trait.

    “for a new phenotype to emerge, new alleles must be formed. In other words, information has to be added to the genome – something genetics tells us doesn’t happen.” I’m still not agreeing with your and Witt’s strange interpretation of information theory. Why the focus on “add”? Is that somehow different than “change”? But back to alleles. The Intro to Genetics article states: “Mutations are random changes in genes, and can create new alleles.”

    “shows that they both have very similar genomes, indicating they are part of the same created kind.” Okay, what kind is that? Back in the non-theology science world, interbreeding fertile offspring shows that the species are not completely reproductively isolated. Very similar genomes shows that they share a recent ancestor.

  19. George says:

    “However, the genes that code for these proteins make up a tiny, tiny fraction of the human or chimp genome, and only SOME of those proteins were studied. Thus, the idea that one can extend that number to the entire genome and say that human and chimp DNA are 99% similar is just absurd.”

    It’s funny that you stopped discussing protein-coding genes at this point. Why don’t you share with us the percentage of similarity for those genes according to the 2005 Nature paper? You cannot say that they only analyzed SOME of those proteins because they sequenced almost the whole stuff.

    The truth is that the typical human protein has accumulated just one change since chimps and humans diverged. There are regions in the
    genome that vary more rapidly because they are not
    functionally restricted (e.g., genes for histones evolve more
    slowly than immunoglobulin genes or pseudogenes).

    When you compare the degree of similarity between several mammals you find that chimps and humans are more closely related to each other than to any other group.

    It is no secret that repetitive regions of the genome mutate much more faster than other sequences. In fact, it
    is the basis of many techniques of DNA fingerprinting which can find differences between humans. So it is not crazy
    to expect some degree of variation in 5-6 million years if
    they change just in a couple of generations.

    You’re oversimplifying things. This article is obviously
    directed toward the public to misinform them, not to have
    an honest scientific discussion. If you’d want to have one
    you would start by learning some genetics. Just because you
    say that G can only pair with C and cite similarity percentages doesn’t make you an expert.

    In science, if you want to be taken seriously, you can’t just say “He was wrong!”. Your proposals need to explain ALL the previous data and the new data. Attacking a theory by itself is not enough. Science generally progresses by building on top of past discoveries. For example, Einstein extended the Newton laws by pointing out that time does not always beat at the same rate. Even though Einstein was right, Newton’s laws still apply for launching space probes. More importantly, Einstein knew the technical details of physics before challenging the accepted theories. He spoke in the same language as them.

    In the case of creationism, it’s a lost battle from the beginning. They’re proposing a non-scientific idea as the explanation of a natural phenomena. “God did it” will never be enough for a real scientist because it has been shown countless times that “God did it” always ends up being explained by some physical process (e.g., vitalism in the XIX century was debunked when urea was chemically synthesized).

  20. A guest post by Greg Mayer at Why Evolution is True (Coyne’s blog) addresses our debate:

    Darwin’s theory of evolution (and ours), unlike that of Lamarck, is variational, rather than transformational: the process of evolution is a change in frequency of different variants within a population, not a transformation of the individuals. Darwin thus made the origin, nature, and inheritance of variation key problems for biology; indeed, for much of the 20th century, evolution and genetics were often taught as a single course at universities.

    Lamarck is the one who used the giraffe as the classic case of transformational evolution.

  21. jlwile says:

    Shooter, I don’t recall saying you are “stupid,” and if I did, I certainly apologize. Now…I have repeatedly called you IGNORANT, but that is a demonstrable fact, based on some of the truly absurd things you say in your comments.

    You don’t understand what I am saying about genetics because you are ignorant about information theory. Is there no end of the subjects you don’t know anything about but still try to pontificate on? If fish evolved into amphibians, the information for building lungs, a new kind of heart, new limbs, etc., etc. would have to appear in the genome. In other words, new information would have to be added. While the Modern Synthesis desperately wants to believe that mutations can do this, genetics stubbornly says that can’t happen.

    Yes, 10 geneticists is a lot when you think of all the possible scientific fields out there.

    Once again, you need to learn how to read, because “Evolution requires one creature to evolve into another” does not mean that the first creature goes away. It simply means you start with the genome of the first creature and end up with the genome of the second creature. The question, “if we’re descended from monkeys, why are there still monkeys?” is not a common creationist argument, and those who ask it don’t understand evolution or creation.

    You certainly DO NOT try to accurately describe my positions, as your nonsensical statements about “one creature to evolve into another” demonstrate. You intentionally try to distort my views to make them easier to argue against, since you can’t argue scientifically against my actual positions. It is a common dishonest technique used by those who cannot support their position with the facts. I actually don’t mind it when you do that, however, since it shows how indefensible your position is and how desperate you are to believe in it.

    “Mutations are random changes in genes, and can create new alleles.” This is certainly true, but that is not enough. Once again, learn to read what I wrote. New alleles that do not add information will not produce any evolution. That’s what genetics (and mutation experiments) demonstrate. Once again, you might have enough faith to argue against the data. I do not.

    “Very similar genomes shows that they share a recent ancestor.” That can certainly be true. In the case of the finches that I had to educate you about, they did share a common ancestor, because they were a part of the same monobaramin. Thus, they adapted into different species. No information was added to the genome, however. This kind of adaptation is well understood and has nothing to do with the kind of evolution for which you vainly try to argue.

  22. jlwile says:

    George, the similarity between a chimp’s protein-encoding genes and a human’s genes is about 96%, according to the 2005 paper. That is significantly lower than the 99% commonly cited, and it is also not surprising. After all, humans and chimps have similar biochemistry, so they use similar proteins. It is also irrelevant to evolution, since the ENTIRE genome is what details all the changes that supposedly took place during the evolution of chimps and humans as they supposedly diverged from their common ancestor. Thus, evolutionists are now faced with the mammoth task of trying to explain how this 30% change occurred. Of course, they will probably do what evolutionists do the best, simply ignore the data and hope they go away!

    It is certainly true that GENETICALLY, when you compare the degree of similarity between several mammals you find that chimps and humans are more closely related to each other than to any other group. However, that is not true MORPHOLOGICALLY. A recent study shows that of 63 morphological characteristics, humans and orangutans share 28, while humans and chimps share only 2. This, of course, is one more data set that shows the confident assertion that humans and chimps are the most closely-related primates is probably not true, and it shows just how little explanatory power evolution provides.

    The article is actually meant to inform the public, since the public has been so misinformed by evolutionists over the years. Evolutionists have confidently asserted that human and chimpanzee genomes are nearly identical. The data clearly show that this is not the case. If you really think evolution is so well-supported by the data, you should not have a problem with these data being communicated. I suggest that you learn genetics so that you have an idea of what these data truly mean.

    The fact that you think creationists just say “he was wrong” and offer a non-scientific idea for origins shows that you haven’t really investigated this issue very much. The creation model is a robust scientific model that has made several predictions which have been later confirmed by the data. Creationists don’t just say, “God did it,” and you are demonstrating your ignorance of this discussion when you suggest that.

    In fact, evolution has lost the battle, because the data show it doesn’t work. That’s why so many scientists are abandoning it.

  23. jlwile says:

    Shooter, Greg Mayer’s description of the current view of evolution is correct, but it is certainly not a correct description of Darwin’s view. Darwin definitely believed in the transformation of individuals, as he believed that direct lineages would be found in the fossils record so much that it would blur the distinction between species.

    Also, Darwin didn’t make “the origin, nature, and inheritance of variation key problems for biology.” Those were problems for biology long before Darwin, and they will still be investigated long after the most die-hard evolutionist finally gives up due to the overwhelming amount of evidence against evolution. Darwin (and current evolutionists) just propose a model within which these things can supposedly be understood. In fact, that’s why so many scientists are abandoning evolution – they see that the model doesn’t work.

  24. “If fish evolved into amphibians, the information for building lungs, a new kind of heart, new limbs, etc., etc. would have to appear in the genome.” Correct, the information did appear in the genome. But it was not added, which you try to liken to newly created out of nowhere. The information for building gills changed into information for building lungs. The information for building fins changed into information for building limbs. Etc.

    You “stubbornly says that can’t happen,” not genetics. You avoid dealing with my questions, the one I have kept repeating in this thread is : how is a mutation “adding” information?

    Here’s a great example of scientific blogging explaining how evolution works, in this case speciation, rather than trying to poke holes in something or other. I actually learned something about natural selection from reading it, as opposed to your posts.

  25. jlwile says:

    “Correct, the information did appear in the genome. But it was not added, which you try to liken to newly created out of nowhere.” I know it is hard for you to think logically, so I will spell it out for you:

    1. It wasn’t there
    2. It now is
    3. Thus, it was ADDED.

    Think about it…take as much time as you want…

    You ask, “how is a mutation “adding” information?” It is not. That is exactly my point. Mutations can’t add information, which is why genetics is the enemy of evolution. Thank you for confirming Lester’s point, which you originally ridiculed. Now you know that you were the one who was being ridiculous. Try to learn from your mistakes this time!

    The link you gave was a really good example of serious research, showing how speciation can be reinforced. If course, it has nothing to do with this discussion, as speciation is not at issue here. It’s not surprising that you don’t even see how this is unrelated to the discussion, since you clearly don’t understand the discussion at all (which you have already admitted). If you actually took the time to seriously look at the data and think about it for a change, you might actually start to learn something. I doubt that you will, however.

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