How ENV muddies the waters on the evidence for human evolution

Recently, Evolution News and Views published an article titled, The Human-Ape Missing Link — Still Missing (July 18, 2017), which attempts to cast doubt on human evolution by quoting from a recent BBC article which highlighted the massive uncertainties that still remain over the identity, appearance and date of the last common ancestor (LCA) of human beings and chimpanzees, and which even questions whether the chimpanzee is our closest relative, after all. The Evolution News and Views (ENV) article also revives the myth of an unbridgeable gap between Australopithecus and Homo.

Here’s my two-sentence rebuttal: uncertainty as to who the last common ancestor of humans and chimps was, what it looked like, and when it lived, in no way diminishes scientists’ certainty that it existed. And while the fossil record of human ancestors is very meager and patchy until about 4.4 million years ago, from that time onward, we have a veritable hodgepodge of hominins – and no unbridgeable gaps.

Well, that was quick, wasn’t it? Now for a more detailed rebuttal.

What’s the best evidence for human evolution?

For those wanting a quick overview of the evidence for human evolution, I would recommend Dennis Venema’s four-part series, titled, Intelligent Design and common ancestry, as well as his five-part series, Vitellogenin and Common Ancestry.

Dennis Venema’s 22-part series, titled, Adam, Eve, and Human Population Genetics, goes on to establish that the ancestral human population has never numbered less than 10,000 during the past one million years. In short: the notion that humanity originally descended from a single couple has been scientifically discredited. After reading Venema’s posts, I have been forced to revise my own views on Adam and Eve. (More about that in a future post.)

Readers who may be inclined to query the alleged 98% genetic similarity between humans and chimps might want to have a look at my Uncommon Descent articles, Human and chimp DNA: They really are about 98% similar and Double debunking: Glenn Williamson on human-chimp DNA similarity and genes unique to human beings. The latter article also deals with the genes which are alleged to be totally unique to human beings, and shows that they are nothing of the sort.

What the BBC article actually said

The BBC article cited in the anonymous Evolution News and Views post on human evolution was refreshingly frank about what we do and don’t know about the last common ancestor of humans and chimpanzees. Here’s how the ENV post summarized its findings:

Here is a long, substantive, and interesting article from the BBC — “We still have not found the missing link between us and apes.” It is interesting for two reasons.

1. It admits that we haven’t found anything that resembles the last common ancestor (LCA) between humans and apes, what author Colin Barras calls the “missing link.”
2. It admits that it’s hard to even agree on what the LCA might have looked like.

Nowhere, however, did the article contest the evidence for human evolution. What it said was that last common ancestor may have looked a lot less chimp-like than most scientists had previously believed, and that we still haven’t found this creature yet.

My major quarrel with the BBC article is that it did not mention any hominin fossils (in the line leading to humans) older than that of the 4.4-million-year-old Ardipithecus ramidus. Older probable hominin fossils such as Ardipithecus kadabba, Orrorin tugenensis, Sahelanthropus tchadensis and Graecopithecus freybergi, which go back as early as 7.2 million years ago, are completely ignored. This is a significant omission, as the human-chimp split is currently estimated to have taken place between 7 and 13 million years ago. If the oldest hominin fossil is 7.2 million years ago, then we are not so far from the last common ancestor, after all.

The allegedly unbridgeable gap between Australopithecus and Homo

The Evolution News and Views article also claims that “we don’t even have transitional forms between Australopithecus and Homo.” This, I have to say, is simply not true.

The article they link to, to support this claim, is an earlier post on Evolution News and Views (“A Big Bang Theory of Homo,” August 13, 2012). Unfortunately, the references cited nearly all date from 1990 to 2007. In recent years, there has been a dramatic shift in scientists’ views.

Until a few years ago, many anthropologists believed that there were stark anatomical differences between Australopithecus and Homo ergaster (pictured above), whose Asian counterpart was Homo erectus. Many of these anthropologists also believed that Homo habilis should be classified as a species of Australopithecus. Oft-cited in this regard is a 2000 paper by J. Hawks, K. Hunley, S.H. Lee, and M. Wolpoff, titled, Population bottlenecks and Pleistocene human evolution (Molecular Biology and Evolution 17(1):2–22), in which the authors write: “We, like many others, interpret the anatomical evidence to show that early H. sapiens was significantly and dramatically different from earlier and penecontemporary australopithecines in virtually every element of its skeleton (fig. 1) and every remnant of its behavior…” In support of their claim, the authors cited the work of Bernard A. Wood and Mark Collard, who put forward powerful arguments for this view in 1999, in their paper, The human genus (Science Vol. 284 no. 5411 pp. 65-71). However, I should mention that while Wood and Collard found major anatomical differences between Homo habilis in six broad categories of traits – body size, body shape, locomotion, jaws & teeth, development, and brain size – three of those traits could not be assessed for another species of early Homo, Homo rudolfensis. Wood and Collard defended their view that Homo erectus represented a clean break from his hominid predecessors once again in their 2001 paper, The Meaning of Homo (Ludus vitalis, vol. IX, no. 15, 2001, pp. 63-74) and more recently, in their 2007 paper, Defining the genus Homo (in Henke, W. and Rothe, H. and Tattersall, I., (eds.) Handbook of Paleoanthropology, Springer Berlin Heidelberg: Berlin, pp. 1575-1610).

However, the scenario proposed by Wood and Collard and is now out of date. Recent papers published in 2012 – see Early Homo: Who, When, and Where (by Susan C. Antón, in Current Anthropology, Vol. 53, No. S6, “Human Biology and the Origins of Homo,” December 2012, pp. S278-S298), Origins and Evolution of Genus Homo: New Perspectives (by Susan C. Antón and J. Josh Snodgrass, in Current Anthropology, Vol. 53, No. S6, “Human Biology and the Origins of Homo,” December 2012, pp. S479-S496) and Human Biology and the Origins of Homo: An Introduction to Supplement 6 (by Leslie C. Aiello and Susan C. Antón, in Current Anthropology, Vol. 53, No. S6, “Human Biology and the Origins of Homo,” December 2012, pp. S269-S277) show that the transition from Homo habilis to early Homo ergaster / erectus was not much larger than that between Australopithecus and Homo habilis. A detailed anatomical comparison indicates that the transition from Australopithecus to early Homo, who appeared about 2.3 or 2.4 million years ago, and from early Homo to Homo ergaster / erectus, is much smoother and more gradual than what anthropologists believed it to be, ten years ago. The above-cited 2012 article by Susan C. Antón and J. Josh Snodgrass, titled, Origins and Evolution of Genus Homo: New Perspectives, conveys the tenor of the new view among anthropologists (emphases mine – VJT):

Recent fossil and archaeological finds have complicated our interpretation of the origin and early evolution of genus Homo. It now appears overly simplistic to view the origin of Homo erectus as a punctuated event characterized by a radical shift in biology and behavior (Aiello and Antón 2012; Antón 2012; Holliday 2012; Pontzer 2012; Schwartz 2012; Ungar 2012). Several of the key morphological, behavioral, and life history characteristics thought to first emerge with H. erectus (e.g., narrow bi-iliac breadth, relatively long legs, and a more “modern” pattern of growth) seem instead to have arisen at different times and in different species

Over the past several decades, a consensus had emerged that the shift to humanlike patterns of body size and shape — and at least some of the behavioral parts of the “human package” — occurred with the origin of Homo erectus (e.g., Antón 2003; Shipman and Walker 1989). This was seen by many researchers as a radical transformation reflecting a sharp and fundamental shift in niche occupation, and it emphasized a distinct division between H. erectus on the one hand and non-erectus early Homo and Australopithecus on the other. Earliest Homo and Australopithecus were reconstructed as essentially bipedal apes, whereas H. erectus had many of the anatomical and life history hallmarks seen in modern humans. To some, the gap between these groups suggested that earlier species such as Homo habilis should be excluded from Homo (Collard and Wood 2007; Wood and Collard 1999).

Recent fossil discoveries paint a picture that is substantially more complicated. These discoveries include new fossils of H. erectus that reveal great variation in the species, including small-bodied members from both Africa and Georgia (Gabunia et al. 2000; Potts et al. 2004; Simpson et al. 2008; Spoor et al. 2007), and suggest a previous overreliance on the Nariokotome skeleton (KNM-WT-15000) in reconstructions of H. erectus. Additionally, reassessments of the Nariokotome material have concluded that he would have been considerably shorter than previous estimates (∼163 cm [5 feet 4 inches], not 185 cm [6 feet 1 inch]; Graves et al. 2010), younger at death (∼8 years old, not 11–13 years old; Dean and Smith 2009), and with a life history pattern distinct from modern humans (Dean and Smith 2009; Dean et al. 2001; Thompson and Nelson 2011), although we note that there is substantial variation in the modern human pattern of development (Šešelj 2011). Further, the recent discovery of a nearly complete adult female H. erectus pelvis from Gona, Ethiopia, which is broad and has a relatively large birth canal, raises questions about the narrow-hipped, Nariokotome-based pelvic reconstruction and whether H. erectus infants were secondarily altricial (Graves et al. 2010; Simpson et al. 2008).

I should add that the average brain size of Homo ergaster / erectus specimens in Africa, dating from 1.8 to 1.5 million years ago, is a mere 863 cubic centimeters, while that of Georgian specimens of Homo ergaster / erectus dating from 1.8 to 1.7 million years ago is even lower, at 686 cubic centimeters (see Susan C. Antón and J. Josh Snodgrass, from Origins and Evolution of Genus Homo: New Perspectives, in Current Anthropology, Vol. 53, No. S6, “Human Biology and the Origins of Homo,” December 2012, pp. S479-S496). By comparison, the brain size of early Homo specimens (excluding 1470 man) is 629 cubic centimeters. [The brain size of 1470 man, or Homo rudolfensis, is variously estimated at anywhere between 526 and 752 cubic centimeters.] Quite clearly, there is no evidence for a sudden jump in brain size from Australopithecus afarensis (whose average brain size was 478 cubic centimeters) to Homo ergaster / erectus. The brain size of early Homo (who lived around 2.3 million years ago) is intermediate between the two.

Is the chimp our nearest relative, or is it the orangutan?

The Evolution News and Views post on the missing link also questions the molecular data linking human beings to chimpanzees, citing the work of Jeffrey Schwartz (who is referred to in the BBC article which it quotes from). Schwartz contends that our nearest relatives are orangutans, not chimpanzees. In a 2009 paper, John Grehan and Jeffrey Schwartz argued that orangutans were morphologically closer humans than chimps were. (See here for a summary of their arguments.) However, another more recent study using a larger dataset found that chimpanzees are morphologically closer to humans than orangutans are (see also here).

The BBC article also pointed out that “few researchers agree with Schwartz.”

In short: the claim that humans are anatomically closer to orangutans appears doubtful. In view of the unequivocal molecular evidence linking humans to chimps, I think it would be prudent to go with the mainstream view that chimps are indeed our closest relatives.

When did humans split off from the line leading to chimpanzees?


Family tree showing the extant hominoids: humans (genus Homo), chimpanzees and bonobos (genus Pan), gorillas (genus Gorilla), orangutans (genus Pongo), and gibbons (four genera of the family Hylobatidae: Hylobates, Hoolock, Nomascus, and Symphalangus). All except gibbons are hominids. Image courtesy of Wikipedia and Fred the Oyster.

Ever since the late 1960s, molecular biologists have argued that humans and chimpanzees last shared a common ancestor around five or six million years ago. Gorillas were subsequently estimated to have diverged from the human-chimp line about seven million years ago. Recently, however, these specialists have revised their dating, and some researchers in the field are now doubling their original estimate of the date of the human-chimp split.

In 2012, a report in Nature by Aylwyn Scally et al. estimated that humans and gorillas last shared a common ancestor 10 million years ago, while humans and chimps diverged around 6 million years ago.

In 2014, however, a new study by Gil McVean et al. (vol. 483, 169–175 (08 March 2012), doi:10.1038/nature10842) suggested a much older date for the human-chimp split. A Live Science report by Charles Quoi (Human and Chimp Genes May Have Split 13 Million Years Ago, June 12, 2014) summarizes the results of the study (emphases mine – VJT):

Past estimates of when the ancestors of humans diverged from chimps suggested the most recent common ancestor of both species lived about 6 million years ago. However, in the past decade or so, genetic analyses revealed the human mutation rate is actually half as fast as was previously thought, suggesting the most recent common ancestor of humans and chimps actually lived at least 12 million years ago.

Now a new study of chimp mutation rates appears to confirm that the most recent common ancestor of humans and chimps lived about 13 million years ago.

“Our results add substance to the idea that the human-chimpanzee split was considerably older than has been recently thought,” said study co-author Gil McVean, a geneticist at the Wellcome Trust Centre for Human Genetics in Oxford, England.

Quoi qualifies his remarks by acknowledging that the new evidence is compatible with the human-chimp split having taken place as recently as 7 million years ago:

Paleoanthropologist John Hawks at the University of Wisconsin-Madison, who did not participate in this study, noted that 13 million years is only the average time for when the genes of the ancestors of humans and chimps diverged; it’s not necessarily when the ancestors of humans and chimps split into different species.

A species divergence of 7 million to 10 million years would be just fine with a genetic divergence averaging 13 million years if the common ancestor population was very large in numbers, or the common ancestor population was spread into different subpopulations with reduced mixing between them,” Hawks said. [8 Humanlike Behaviors of Primates]

McVean agreed with Hawks’ analysis. If the size of the ancestral population of both humans and chimps was very large, then their common gene pool may have begun diversifying long before the ancestors of humans and chimps split into different species, he said.

In the last year, more recent research has lent further support to the view that humans and chimps may have split up to 12 million years ago. I’ll mention just two articles:

(1) Variation in the molecular clock of primates (PNAS, September 20, 2016; 113(38): 10607–10612) by Priya Moorjani, Carlos Eduardo, G. Amorim, Peter F. Arndt and Molly Przeworskia:

Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years,​ and the human and gorilla divergence time is 15.1 million years​.

(2) New geological and palaeontological age constraint for the gorilla–human lineage split (Nature, vol. 530, pp. 215–218 (11 February 2016) doi:10.1038/nature16510) by Shigehiro Katoh et al., argues strongly that humans last shared a common ancestor with the gorilla at least 8 million years ago, and possibly 10 million years ago:

The palaeobiological record of 12 million to 7 million years ago (Ma) is crucial to the elucidation of African ape and human origins, but few fossil assemblages of this period have been reported from sub-Saharan Africa. Since the 1970s, the Chorora Formation, Ethiopia, has been widely considered to contain ~10.5 million year (Myr) old mammalian fossils. More recently, Chororapithecus abyssinicus, a probable primitive member of the gorilla clade, was discovered from the formation. Here we report new field observations and geochemical, magnetostratigraphic and radioisotopic results that securely place the Chorora Formation sediments to between ~9 and ~7 Ma. The C. abyssinicus fossils are ~8.0 Myr old, forming a revised age constraint of the human–gorilla split. Other Chorora fossils range in age from ~8.5 to 7 Ma and comprise the first sub-Saharan mammalian assemblage that spans this period. These fossils suggest indigenous African evolution of multiple mammalian lineages/groups between 10 and 7 Ma, including a possible ancestral-descendent relationship between the ~9.8 Myr old Nakalipithecus nakayamai and C. abyssinicus

The authors are uncertain as to whether Nakalipithecus nakayamai lived just before or just after the split between the gorilla lineage and the line leading to humans and chimps.

So at the moment, any date between 7 and 12 million years appears possible, for the human-chimp split. For my part, I’ll go with a date of 8 or maybe 9 million years for the human-chimp split, and 10 to 12 million years for the split between gorillas and the human-chimp line. I should mention that a date of 8 million years for the human-chimp split would push back the date of the split between orangutans and the other great apes to as early as 20 million years ago, which is about as early as the fossil evidence will allow.

Who was the last common ancestor, anyway?

Curiously, the BBC article cited by ENV says nothing about Sahelanthropus tchadensis (pictured above and at the top of this post), a hominin who lived 7 million years ago in Chad. Its discoverers claimed that it was a very ancient human ancestor but not a chimpanzee ancestor; however, some experts now believe it may have been the common ancestor of humans and chimps – or a very near relative.

Another possible candidate for the last common ancestor of humans and chimps is Graecopithecus freybergi, who lived on the savanna in Greece about 7.2 million years ago. However, a detailed examination of the morphology of the molar teeth associated with two fossils of Graecopithecus freybergi published in 2017 suggests that it may be a hominin, although other experts are skeptical.

Finally, Oreopithecus bambolii, an extinct hominoid primate discovered in the 1950s that lived in Italy from 9 to 7 million years ago, has been proposed by some as a human ancestor, although most scientists view it as an ape who was not part of the human lineage, and regard its anatomical resemblances to humans (notably in its hands) as an example of convergent evolution. To this day, the creature’s taxonomic status remains hotly disputed.

To sum up: the last common ancestor of humans and chimps may have already been found. But if the human-chimp split occurred 8 or 9 million years ago, the existence of possible hominin fossils from 7.2 million years ago is definitely a hopeful sign.

Conclusion

Despite the many uncertainties regarding the timing of the human-chimp split and the identity and appearance of the last common ancestor, scientists are justifiably confident that the chimpanzee is our closest relative. There is no good evidence for a “Big Bang” in human evolution, as far as the evolution of the human body is concerned; nor was there a time when our brain size suddenly increased. To sum up: the recent ENV article, which uses the absence of the missing link in order to cast doubt on human evolution, is profoundly misguided.

268 thoughts on “How ENV muddies the waters on the evidence for human evolution

  1. newton: Irony abounds

    So does turning a blind eye. I’m pretty sure this site exists as a satire.

    #TheSatiricalZone

  2. Mung: So does turning a blind eye.

    Thought you were anti-moderation

    I’m pretty sure this site exists as a satire.

    #TheSatiricalZone

    You certainly are doing your part

  3. colewd:
    vjtorley,

    Do you think this claim is wrong?If it is not then the 1-2% claim is suspect.

    I swear we’ve been over this before. There are many possible measures of genetic similarity. If you pick percent difference in aligned sites, humans and chimps are 1.23% different. If you count each base in every indel as a difference, humans and chimps are about 5% different. But the latter is a stupid and useless measure, since it counts an indel of a thousand bases, a single mutation, as a thousand differences. How does that make any sense? The claim is not so much wrong as pointless.

  4. John Harshman: There are many possible measures of genetic similarity.

    I like to go by whether the chromosomes are different. By my measure humans and chimps are 100% different.

  5. I say we ignore everything we know about how genomes mutate and diverge and go with Mung’s chromosomal metric instead. Having an extra pair of them he must know what he’s talking about

  6. Mung: I like to go by whether the chromosomes are different. By my measure humans and chimps are 100% different.

    By your measure, there cannot be such a thing as degree of difference. Either things are identical or they are not. As such it is not really a “measure”, but a dichotomy.

    With your “measure”, you would find one-egged twins “100% different” just as you would a Greenland inuit and a sub-Saharan African.

  7. The point about the difference between human and chimp genomes is not whether it is 1.23% or 5%. John H has succinctly explained why one could get either of those figures, depending on how one calculates the difference.

    The point is that whatever definition of distance one uses, chimp and humans turn out to be less different than chimp and gorilla. And all three less different than any is to orang. And so on. And that’s an incredibly robust result, whatever the Discovery Institute thinks.

  8. Joe Felsenstein,

    The point is that whatever definition of distance one uses, chimp and humans turn out to be less different than chimp and gorilla. And all three less different than any is to orang. And so on. And that’s an incredibly robust result, whatever the Discovery Institute thinks.

    The theory of biological relativity 🙂

  9. John Harshman,

    . But the latter is a stupid and useless measure, since it counts an indel of a thousand bases, a single mutation, as a thousand differences. How does that make any sense? The claim is not so much wrong as pointless.

    Does anyone have data on how many indels there are or have been identified. How do you judge that the mutational group is an indel?

  10. newton,

    What is your explanation for the observation?

    Still working on it. Einstein took 10 years on general relativity 🙂

  11. Rumraket,

    How can you even be asking that?

    I was not aware that we had access to the common ancestors DNA 🙂

    I think there should be a procedure for determining indels. If you know it please feel free to share.

  12. Mung: Somehow you managed to gain access to your parent’s DNA.

    Is that a plausible hypothesis? because I have an innumerable amount of alternatives… like for instance, that it was actually his uncle’s DNA… oh wait..

  13. colewd:
    John Harshman,

    Does anyone have data on how many indels there are or have been identified.How do you judge that the mutational group is an indel?

    If I recall, there are around 5 million indels separating the human and chimp genomes. I don’t know what a “mutational group” might be, but it’s an indel if it’s present in one species but absent in the other, that is, the alignment of some portion of one genome must have a gap of some number of bases in order to be aligned with the other genome. The term “indel” is short for “insertion or deletion”.

  14. John Harshman,

    If I recall, there are around 5 million indels separating the human and chimp genomes. I don’t know what a “mutational group” might be, but it’s an indel if it’s present in one species but absent in the other, that is, the alignment of some portion of one genome must have a gap of some number of bases in order to be aligned with the other genome. The term “indel” is short for “insertion or deletion”.

    So 3 plus percent on the 5% total difference is indels. 100 million bp divided by 5 million is 20bp average length per indel. Are these indels repetitive DNA? Could they be responsible for changes in gene expression?

  15. OMagain: Ever been to the zoo, Robert?

    Thats my point.
    Comparing zoo chimps with people is JUST THAT. Comparisonism.
    Its not biological investigation. its just a hunch rejecting other options within hunch spectrum.
    Your making the mistake evolutiondom made and makes.
    Comparative anatomy and genetics is not about biological processes. its only about a STATE of being AFTER biological processes have happened.
    YET they claim that using this STATES of being counts as investigating biological processes with conclusions about biological origins.
    Its a grand slam error in science investigation.

  16. Hi colewd,

    Regarding the ENV article, In Arguments for Common Ancestry, Scientific Errors Compound Theoretical Problems (May 16, 2016), you ask:

    Can you show me where you think the arguments in the above paper are flawed?

    Happy to oblige. Let me focus on just one argument: number 2. The author writes:

    (2) There’s good evidence that genetic differences between humans and chimps could not arise by standard evolutionary mechanisms.

    Let’s assume for the sake of argument that Dr. Swamidass is correct that mice and rats are about 15 percent genetically different whereas humans and apes are only 1.5 percent different. The much bigger problem is that even in humans and chimps, those few percent differences still equate to tens of millions of base pair differences, plus millions of larger differences that entail indels, etc. And when we’re looking at humans and chimps, if just two of those specific differences were required before giving any functional advantage, then that would have taken over 200 million years to arise. So even very small genetic differences can still take a long time to arise. Casey Luskin explains here, writing in response to Dennis Venema’s similar argument:

    …In 2008, Michael Behe’s critics Rick Durrett and Deena Schmidt tried to refute him in the journal Genetics with a paper titled “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution.” But Durrett and Schmidt found that to obtain only two specific mutations via Darwinian evolution “for humans with a much smaller effective population size, this type of change would take > 100 million years.” The critics admitted this was “very unlikely to occur on a reasonable timescale.”

    In other words, if any of the 35 million base pair changes between humans and chimps entail adaptive changes that require two or more specific mutations before providing any advantage, then they would be extremely unlikely to evolve by random mutation and natural selection in the mere 6 or 7 million years since we shared our alleged most recent common ancestor with chimps.

    Durrett and Schmidt found that it would take too long to wait for two specific mutations to gain an advantage. How does Venema know that there aren’t many differences between humans and chimps that would require two (or perhaps many more — dozens, hundreds, millions?!) mutations before any benefit arises?

    Luskin is reversing the onus of proof. Instead, what I would ask him is the same question I posed to Dr. Axe: can you identify a single case in the line leading to human beings, where two or more mutations had to act in combination, in order to confer an increase in fitness in our ancestors? No? So much for Durrett and Schmidt, then.

  17. colewd:
    John Harshman,

    So 3 plus percent on the 5% total difference is indels.100 million bp divided by 5 million is 20bp average length per indel.Are these indels repetitiveDNA?Could they be responsible for changes in gene expression?

    Some indels are repetitive DNA. Some are not. Some indels (around half) are deletions. The avarage length may be 20bp, but the great majority of indels are 1bp. A few indels probably result in changes in gene expression, just as do a few point mutations. But of course the bulk of indels happen in junk DNA. Still have those straws clutched in your fist, eh?

  18. vjtorley,

    You wrote that entire section, to say Casey Luskin has reversed the burden of proof , AND THIS IS WHY the arguments in the paper are flawed (because you would have asked the question differently) and thus (anti-ID) scientists Richard Durrett and Deena Schmidt findings are invalid.

    You are a riot.

  19. Acartia: I must have been missing from class the day they told us that anatomy and genetics weren’t part of biology.

    Anatomy and genetics is only the end game AFTER biological processes have occurred.
    Yet in biological origin research it demands biological evidence for processes.
    Using the finished results as evidence for the processes is wrong bio investigation policy. Its not science.
    Biological origins with a evolutionist hypothesis must be demonstrated with biological processes.
    Not biological results after the fact.!!
    Anatomy can not be used for common descent claims. nor genetics.
    Both are independent of the origin of their results. They are silent.
    Its a great error in thinking to say they are evidence for processes.
    Ape/human likeness is not biological evidence for common descent.
    its just a line of reasoning from presumptions when other options exist.

    Your side must prove why anatomy and genetics are independent sources of evidence for biological processes!!
    They are not biological processes but end results OF BIOLOGICAL PROCESSES.
    They are not evidence of common descent even if CD was true and they were the end results of it.
    In complicated things scientific investigation must be sharp and on the ball.

  20. vjtorley,

    Furthermore, all Luskin said was “IF” only two. That’s not reversing any burden of proof, the theory of evolution is what is being argued, not the theory of ID. So if we are arguing about the theory of evolution’s ability to go from chimps to humans, OF COURSE the burden of proof has to be on evolutionists to show that it could happen. Evolutionists always want to just throw out the nonsense defense, “Well, prove it couldn’t…” as if this is some great barrier defense.

    If all a scientific theory needed to do was be protected from you proving it COULDN’T happen, then believe me, I can think of a whole lot of explanations for the existence of chimps and men, that you can’t prove isn’t true, including them being carried here by a bunch of snorkel laden jackasses from Uranus.

  21. phoodoo:
    Furthermore, all Luskin said was “IF” only two.That’s not reversing any burden of proof, the theory of evolution is what is being argued, not the theory of ID.So if we are arguing about the theory of evolution’s ability to go from chimps to humans, OF COURSE the burden of proof has to be on evolutionists to show that it could happen.Evolutionists always want to just throw out the nonsense defense, “Well, prove it couldn’t…” as if this is some great barrier defense.

    If all a scientific theory needed to do was be protected from you proving it COULDN’T happen, then believe me, I can think of a whole lot of explanations for the existence of chimps and men, that you can’t prove isn’t true, including them being carried here by a bunch of snorkel laden jackasses from Uranus.

    Surprisingly, and somewhat ironically, there’s a good point buried here. “You can’t prove me wrong” is NOT support for any proposed explanation of anything. Support must be positive, never negative.

    So while it’s not “the theory of evolution’s ability to go from chimps to humans” (what a strange locution that is), it is the case that whatever explanation is provided for how humans and chimps could have diverged from a common ancestor, should be supported by some testable mechanism. As in fact it is, and very solidly supported.

    Now, ID is composed ENTIRELY of “you can’t prove me wrong.” Although sometimes it’s supported by “if I can misrepresent your theory ignorantly enough, my unsupported claims must be right be default.”

  22. Joe Felsenstein:
    The point about the difference between human and chimp genomes is not whether it is 1.23% or 5%.John H has succinctly explained why one could get either of those figures, depending on how one calculates the difference.

    The point is that whatever definition of distance one uses, chimp and humans turn out to be less different than chimp and gorilla.And all three less different than any is to orang.And so on.And that’s an incredibly robust result, whatever the Discovery Institute thinks.

    Its a robust result of likeness but the subject is about evolution.
    If your saying likeness equals proof of common descent then you have a good point.
    If your saying likeness proves biological processes that prove a common descent THEN you have a poor point.
    Its not biological scientific investigation into evolutionary origins but only a simple comparitivology bereft of biological evidence.
    Your crowd is just saying people/primate likeness proves evolution but creationism would predict this too with no relationship on common descent.
    Evolutionism can’t forever get away with poor scholarship on science methodology.
    A hunch is not good enough.

  23. phoodoo: Robust? Are you serious?

    Not only is saying, “well, it could be 1 percent or maybe 3 or 5, but more than other animals probably”, not only not robust, its even debatable whether or not its even true.

    [snipped link to article about orangutang study]

    The article reported that humans were more closely related to chimps than to orangutangs. It did say some regions of the DNA showed the orangutangs more closely related. This is expected from random trees of gene copies (“coalescents”), given that copies in a population are variably related to each other. It is not a shock, a surprise, or a discrepancy.

    on “common design”:

    Yup, any pattern in nature we see could be “common design”. It explains why elephants are big, gray, and lumber around the savannah eating bushes. Alas, it also explains why elephants are small, pink, and flit from flower to flower pollinating them. Which somewhat limits taking it seriously as a scientific explanation.;

  24. Joe Felsenstein: It explains why elephants and big, gray, and lumber around the savannah eating bushes. Alas, it also explains why elephants are small, pink, and flit from flower to flower pollinating them. Which somewhat limits taking it seriously as a scientific explanation.;

    And evolution doesn’t explain it??

  25. colewd: I think there should be a procedure for determining indels. If you know it please feel free to share.

    Ok.

    From speices A: AAGTGTGGGGTCCCTCGTA
    From speices B: AAGTGTGGGTCCCTCGTA
    From speices C: AAGTGTGGGTCCCTCGTA

    Oh gee I can’t figure out what kind of mutation happened here. We must have the common ancestor to find out, otherwise evolution is implausible and design wins by default.

  26. Flint,

    How to test it.

    I have heard this line a million times. But never heard a real answer. Saying if there are no rabbits found in the Cambrian, that tests it, is not a real answer.

  27. phoodoo: Evolutionists always want to just throw out the nonsense defense, “Well, prove it couldn’t…” as if this is some great barrier defense.

    Ever since Darwin. I actually caught one in the act of doing this. I’ll try to find it and post it.

  28. Rumraket: How to test what, specifically?

    Intelligence. Or lack of it. We want to know just how intelligent The Designer is and just how unintelligent evolution is.

  29. Flint,

    So while it’s not “the theory of evolution’s ability to go from chimps to humans” (what a strange locution that is), it is the case that whatever explanation is provided for how humans and chimps could have diverged from a common ancestor, should be supported by some testable mechanism. As in fact it is, and very solidly supported.

    Can you articulate further how you think this transition is supported?

  30. Rumraket,

    From speices A: AAGTGTGGGGTCCCTCGTA
    From speices B: AAGTGTGGGTCCCTCGTA
    From speices C: AAGTGTGGGTCCCTCGTA

    Oh gee I can’t figure out what kind of mutation happened here. We must have the common ancestor to find out, otherwise evolution is implausible and design wins by default.

    What is your conclusion from observing the above sequences, Are you saying they are indels?

  31. colewd: Rumraket,

    From speices A: AAGTGTGGGGTCCCTCGTA
    From speices B: AAGTGTGGGTCCCTCGTA
    From speices C: AAGTGTGGGTCCCTCGTA

    Oh gee I can’t figure out what kind of mutation happened here. We must have the common ancestor to find out, otherwise evolution is implausible and design wins by default.

    What is your conclusion from observing the above sequences, Are you saying they are indels?

    Ok, let me spell it out. Indels mean insertions-deletions as Harshman already pointed out. Which means either something has been added (the sequence was made longer), or it was deleted (the sequence was made shorter). They’re not mutually exclusive, a sequence can be made shorter by having something deleted in one position, and longer by having something added in another position.

    With that in mind, look at the three sequences and compare them. They’re identical except two of them B and C are shorter than A. What is the simplest explanation using observed mechanisms, for this observation? That an insertion has happened in A (therefore an indel). Why is that the simplest explanation? Because the only other possible explanation is that two deletions have happened independently in B and C in the same position. A single insertion is simpler than two deletions. One mutation is simpler than two mutations.

    It is super simple to infer that indels have happened. Simply look at the sequences and compare them. Align the positions that align, see if there are gaps. If there are gaps, then indels have happened. That is pretty much it.

  32. Rumraket: Why is that the simplest explanation? Because the only other possible explanation is that two deletions have happened independently in B and C in the same position. A single insertion is simpler than two deletions. One mutation is simpler than two mutations.

    Circular reasoning. Why is that the simplest explanation? Because that’s the simplest explanation. That’s your argument, lol.

  33. Mung: Circular reasoning. Why is that the simplest explanation? Because that’s the simplest explanation. That’s your argument, lol.

    No ,because of the definition of simple.

  34. Mung,

    Circular reasoning. Why is that the simplest explanation? Because that’s the simplest explanation. That’s your argument, lol.

    Based on the a priori assumption there is a material explanation. And based on the a priori assumption of universal common descent. And based on the a priori assumption that the simplest explanation is always the right one. And based on the assumption that an indel is easier then two deletions.

  35. colewd: And based on the assumption that an indel is easier then two deletions.

    That doesn’t even make sense, lol.

    Did you mean a single insertion is simpler than two deletions because Rumraket says so? Or that two mutations are more complex than one single mutation, because Rumraket says so?

  36. colewd:
    Mung,
    Based on the a priori assumption there is a material explanation.And based on the a priori assumption of universal common descent. And based on the a priori assumption that the simplest explanation is always the right one.And based on the assumption that an indel is easier then two deletions.

    None of these are assumptions except for the first. Yes, one assumes there is a material explanation because otherwise science is unable to function at all. The “explanation” that a miracle occurred doesn’t lead anywhere, which is why, upon finding a safe drilled open and empty, the police don’t decide that God took the money and close the case. Still, if you have a different explanation, I sure wish you would say what it is.

    As for universal common descent, how many times do I have to explain that it’s completely unnecessary to consider universal common descent when local common descent is under discussion, and that it’s not an assumption anyway but a conclusion from data. You have been invited repeatedly to present an alternative hypothesis and have never done so.

    Nor is there an assumption that the simplest explanation is the right one, just that it’s the most probable. Your final objection is in fact the same objection in different words. Yes, one insertion is easier than two deletions. (Incidentally, “indel” refers to either, so you can’t use it as a synonym for “insertion”.) While it’s true that one may be more common than the other, and that this varies fro species to species — the sort of thing one can learn from sequence data — the bias is never all that strong.

    Now in fact it’s entirely possible that a set of sequences like Rumraket describes could be due to two deletions. The way to test that is by comparing more sequences of more individuals or species for clues on how the species are related and what happened to the sequences in question in between the species shown. Since he just made those sequences up, that isn’t going to happen, but that’s how it would work in practice. More likely than not, such additional research would show that there had indeed been a single insertion. But two deletions are certainly possible.

    But more importantly, can’t you do anything other than snipe? Two deletions would be evolution just as much as one insertion would. You’re just attacking to be attacking, and you haven’t considered for one moment the implications of what you say.

  37. John Harshman: None of these are assumptions except for the first. Yes, one assumes there is a material explanation because otherwise science is unable to function at all. The “explanation” that a miracle occurred doesn’t lead anywhere…

    John is terribly confused.

  38. Mung: Rumraket: Why is that the simplest explanation? Because the only other possible explanation is that two deletions have happened independently in B and C in the same position. A single insertion is simpler than two deletions. One mutation is simpler than two mutations.

    Circular reasoning. Why is that the simplest explanation? Because that’s the simplest explanation. That’s your argument, lol.

    There is no circular reasoning there.

    I gave an explanation for why it is the simplest explanation. Because a hypothesis with one instead of two mutations, is a hypothesis that invokes fewer explanatory events to account for the data.

    This would be true even if the sequences were designed. It would be a simpler design hypothesis that the designer simply made and then copied a sequence two times, then made an indel in one, than it would be if he copied a sequence two times and made an indel in two. It’s still a simpler explanation even on design.

  39. John Harshman: But more importantly, can’t you do anything other than snipe? Two deletions would be evolution just as much as one insertion would. You’re just attacking to be attacking, and you haven’t considered for one moment the implications of what you say.

    It has become clear to me that I have really got on the bad side of Mung and Phoodoo, so now they’re in this state of mind where everything I say has to be contradicted regardless of how sensible and basic it is.

    Either they despise me so much they lose the ability to understand plain text if it follows my name, or they’re just trolling because they are butthurt. Whichever it is, it’s fine with me. I trust that a rational person coming to this discussion looking at our exchange can see which of us is making the most sense.

  40. Mung: John is terribly confused.

    But alas, you forgot to explain how, or about what. That leaves other readers lacking your particular insight baffled.

  41. Rumraket: It has become clear to me that I have really got on the bad side of Mung and Phoodoo, so now they’re in this state of mind where everything I say has to be contradicted regardless of how sensible and basic it is.

    Either they despise me so much they lose the ability to understand plain text if it follows my name, or they’re just trolling because they are butthurt. Whichever it is, it’s fine with me. I trust that a rational person coming to this discussion looking at our exchange can see which of us is making the most sense.

    I don’t think you should bother trying to explain evolution to them. Their problem is much more fundamental: they don’t understand basic reasoning, all they do is pull one fallacy after another, unable to logically connect ideas or evaluate their implications. They’re not worth your time

  42. dazz: I don’t think you should bother trying to explain evolution to them. Their problem is much more fundamental: they don’t understand basic reasoning, all they do is pull one fallacy after another, unable to logically connect ideas or evaluate their implications. They’re not worth your time

    I don’t think so, and I don’t think you think so either. They understand basic reasoning perfectly well — if they did not, they couldn’t function well enough to use this site or apply language. Their situation is, they KNOW that evolution doesn’t happen the way theory says — that is, independently of some invisible but necessary guiding hand equipped with both the power to steer biology and some long-range goal to steer toward.

    Their problem, then, is that the evidence saying otherwise is both enormous and consistent, so this must be denied. If this requires word games, or non sequiturs, or mockery, or insults, or missing the point, or changing the subject, well, these are the necessary tools of their trade.

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