Well, that didn't take long. I regretfully report that T_aquaticus wasted little time in proving my proving point that ID proponents are regularly mistreated online, and thus it makes sense why ENV would choose to avoid the hassle of dealing with constant harssment and not allow comments.
Look at t_ T_aquaticus's comments about the "outright lies" and "misleading" arguments of ID proponents that no “honest” person would make.
Unfortunately this is common stuff from ID-critics: ID proponents constantly face accusations that they must be morally dishonest/lying, or ignorant/incompetent. With Ann Gauger, T_aquaticus takes the "ignorant/incompetent" tack. With the ENV article he disagreed with, he takes the "dishonest/lies" tack. I’ll discuss both examples below and show that not only are his ad hominem attacks inappropriate, his arguments are also wrong.
It's fine to disagree with ID people, but why the need to make it so personal and ad hominem? Why not just state your reasons and evidence for disagreeing and leave it there? Why the need to constantly attack people personally? Why not just say "I think they're wrong for X, Y, and Z" and stop there?
I commend Ann Gauger for ignoring the “disses” and noting that ID people aren't perfect either—she’s right, we're all capable of getting too personal sometimes, and ID proponents sometimes are uncivil too, unfortunately. But this is not a situation where there is equality or balance in offensiveness. There is systematic online bullying and oppression of ID proponents in online discussion forums, which often scares them off from forums. It's happening in this forum before your very eyes--and this is supposed to be a Christian forum which holds people to a high standard of civility!
To ignore the problem or simply say “well, everyone does it” would be like saying that if sometimes women harass men, that therefore there's really no issue with men harassing women (as has been in the news lately!). Sure, bad behavior can come from anyone--we're all capable of it. But that doesn't mean there isn't a gross imbalance in the amount of personal attacks/uncivil disses that ID people receive vs. what they dish out. The imbalance is on the receiving end. Again, we see it here.
Sure, these are plenty of times when people make flippant comments online and get nasty. Those kinds of things are easy to overlook. But distressingly, there's even a serious imbalance in the offensiveness of the carefully thought out words that ID-critics choose to put in their books and scientific articles.
To repeat what I said earlier, look at what Dennis Venema said in Adam and the Genome—trying to put ID proponents into the same "dishonest/ignorant" vice that T_aquaticus uses, though using slightly less inflammatory language--or just quoting other people using inflammatory language, and then endorsing those quotes.
For example, consider Dennis Venema's lengthy quote from Dr. Todd Wood he offers on page 41 of Adam and the Genome where Dr. Wood says that anti-evolutionists act "pompously" while being “clueless,” “unacquainted with the inner workings of science,” “unacquainted with the evidence” or maybe even “deluded or lying”.
Wood is a well-qualified young earth creationist biologist, and Venema seemingly endorses what Dr. Wood says in that quote, as Venema writes of Wood's quote immediately after providing it: “he has my sincere respect for his stance.” (p. 41)
These are not poorly thought-out blog comments. These are words that Venema carefully chose to include in Adam and the Genome: He just endorsed the words of a trained biologist stating that many creationists/ID proponents are “pompou[s],” “clueless,” “unacquainted with the inner workings of science,” “unacquainted with the evidence” and maybe even “deluded or lying”. This apparently is what he wants his readers to think.
There's other stuff like this in Adam and the Genome which I documented earlier, such as:
- Venema trying to cast Steve Meyer and the whole body of "antievolutionary scholars" as ignorant and incompetent:
"Meyer's confident assertions aside, antievolutionary scholars have not yet mounted a convincing response to population genetics evidence, nor is it clear that they will be able to do so, since there does not appear to be anyone in the antievolutionary camp at present with the necessary training to properly understand the evidence, much less offer a compelling case against it." (Adam and the Genome, page 65)
"to date, no one in the creationist camp writing about these data seems to understand the evidence, much less has the ability to credibly undermine it” (page 205)
"Interestingly, there are many known cases of exactly this, though Meyer does not seem to be aware of them, or of the implications they hold for his line of argument." (pages 84-85)
- Venema implies Meyer is untrustworthy and that people should not "take him at his word":
"The average layperson who reads Meyer's works, however, may simply take him at his word that scientists have concluded that functional, folded proteins in general are exceedingly rare and thus agree with his assessment that they cannot be produced by natural mechanisms." (page 84)
- Venema attacks "antievolutionary organizations" who make certain arguments about Mitochondrial Eve and Y-Chromosome Adam as either being ignorant, or dishonestly withholding information from the public:
"Unfortunately, many antievolutionary organizations like to promote Mitochondrial Eve and Y-Chromosome Adam without explaining these issues. Typically, it is enough for them to state that they are respectively the common female ancestor for all women and the common male ancestor for all men, to claim (or merely imply) that these data are consistent with Adam and Eve being the sole parents of all humans, and to leave it at that. Thus, for their case to seem plausible, they count on their audience not completely understanding how these types of DNA are inherited--or perhaps they misunderstand it themselves." (page 65)
- It’s not just Venema who apparently has this problem of a condescending tone. A reviewer of Adam and the Genome at The Gospel Coalition found that Venema’s co-author, Scot McKnight, suffers from the same problem of writing accusatorily and condescendingly towards those who disagree with him. Quite strikingly, this reviewer wrote:
"On the rhetorical front, McKnight has a tendency to write dismissively (and condescendingly) about those who disagree with him on Adam. Reading him, you wouldn’t think there are thoughtful or measured reasons for taking the traditional position. It’s as if from Augustine onward, dopy theologians were dishonestly exegeting the Bible, inventing syllogisms to invest Adam with salvific import, glibly conflating modern concerns with the biblical text. This patronizing tone weakens McKnight’s argument. Given how most of the tradition stands against him, I can understand why he may (subconsciously?) have felt the need to strong-arm his way through the argument—but it comes off the wrong way." (https://www.thegospelcoalition.org/article/book-review-adams-genome)
- There's also Dennis Venema claiming that Steve Meyer has an "undergraduate" level of understanding of biology in a paper he published in PSCF. I already quoted it in a previous comment and don't need to quote it again.
Again, these aren’t mere passing blog comments. These were carefully chosen words that were put into a book for the general public (and a paper in a Christian journal). Where’s the high level of civility that BioLogos claims to uphold? Dennis Venema is welcome to argue against intelligent design and creationism, but does he owe an apology to his fellow Christians whose competency and honesty he has repeatedly attacked publicly?
OK, let’s look at the substance of T_aquaticus’s objections:
Regarding Ann Gauger’s BIO-Complexity paper (http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1) he writes:
For example, in this article they made such fundamental errors in modeling evolution that no peer reviewer in any respectable journal would have recommended the paper for publication. They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor. If they wanted to truly model the evolution of the protein then they should have constructed a consensus sequence using a phylogeny of many related species, and then mutated that consensus sequence. They didn't. This is such a basic mistake that it could only pass peer review in an echo chamber.
Frst off, they weren’t modeling the evolution of “species” but rather the evolution of proteins, though I think you are aware of this. Ann Gauger's responses in this forum are good, but it should be known that she responded publicly to this objection years ago in response to another critic who made the exact same arguments:
McBride’s main complaint is that we picked an unnatural evolutionary transition to test. We chose to examine how hard it would be to get a modern-day enzyme to switch to the chemistry of a closely related modern-day enzyme, with very similar structures and catalytic mechanisms.
The reason for our choice was not ignorance. We knew that the enzymes we tested were modern, and that one was not the ancestor of the other. (They are, however, among the most structurally similar members of their family, and share many aspects of their reaction mechanism, but their chemistry itself is different.) We also knew that in order for a Darwinian process to generate the mechanistically and chemically diverse families of enzymes that are present in modern organisms, something like the functional conversion of one of these enzyme to the other must be possible. We reasoned that if these two enzymes could not be reconfigured through a gradual process of mutation and selection, then the Darwinian explanation of gene duplication and gradual divergence to new functions was called into question.
Our results indicated that a minimum of seven mutations would be required to convert or reconfigure one enzyme toward the other’s function. No one disputes that part of our research. What Paul McBride and others claim is that because we didn’t start from an “ancestral” enzyme, our results meant nothing. They say something like, “Of course transitions to new chemistries between modern enzymes are difficult. What you should have done is to reconstruct the ancestral form and use it as a starting point .”
So the answer to T_aquaticus is very simple: Gauger and Axe didn’t intend to test a real-world evolutionary transition. They intended to test the argument that it should be very easy to convert between the functions of two very closely related proteins.
True, these modern-day proteins are paralogs, or close cousins if you will, and not ancestor-descendants. But they’re very similar and very closely related, which makes them ideal for testing the evolutionary claim that closely related proteins should be able to easily evolve new functions that entail small-scale changes to sequence.
In fact, Gauger and Axe explained this exact point in their paper:
A reasonable assumption, consistent with methods used for reconstructing evolutionary histories, is that enzyme pairs with high structural similarity should be most amenable to functional conversion. Whether or not a particular conversion ever occurred as a paralogous innovation (or the direction in which it occurred if it did) is not the point of interest here. Rather, the point is to identify the kind of functional innovation that ought to be among the most feasible within this superfamily and then to assess how feasible this innovation is.
Please note the phrase "Whether or not a particular conversion ever occurred as a paralogous innovation (or the direction in which it occurred if it did) is not the point of interest here." That shows they were directly aware that they were not necessarily testing an evolutionary transition that actually happened in the real world. They disclosed this in the paper, but justified their experimental model nonetheless as a good test of claims about the evolutionary ease of protein innovation.
Moreover, they justify their choice of using two modern-day paralogous enzymes in this paper: They chose two enzymes that are closely related (not ancestral, obviously) to one-another, and thus they use this fact as a test of the hypothesis that it should be easy to convert one enzyme into the function of another similar, closely related enzyme.
So whether or not this was a real-world evolutionary transition is actually irrelevant to their paper or the merits of their findings. The point is that evolutionists believe that functional transitions between two similar enzymes, much like these two, should be a very modest feat for selection and mutation to produe, and the sort of evolutionary change that can happen all the time. They found that such a transition would actually require many mutations before providing some advantage--so many to make it evolutionarily infeasible.
Thus, T_aquaticus’s charges that they didn't unerstand this ("<>") are false. So are his charges that the paper’s reviewers (peace be upon them, whoever they are) let a mistake slide by. So are his personal attacks.
Now, let’s talk about the ENV post by Jonathan M. (https://evolutionnews.org/2011/05/do_shared_ervs_support_common_/) that T_aquaticus takes issue with. To reiterate, he charged that the ENV blog post is “misleading,” has “outright lies” and that the author is not “honest”.
Now as for the substance, the ENV article quotes Yohn et al. 2005 stating:
Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes.
T_aquaticus replies here on this thread:
there were no PtERV1 insertions that violated a nested hierarchy in the Yohn et al. (2005) paper, even though the author of the ENV article claims there were. I would also suggest that you read the Yohn paper and the ENV article and decide for yourself if an honest person would portray the Yohn paper in that manner.
Hmmm—I read Yohn et al. 2005 and came to a very different conclusion, which I will back below with multiple quotes from the paper. Looking at the paper, it quite clearly explains that the ERV (PTERV1) distribution data they examined “is inconsistent with the generally accepted phylogeny of catarrhine primates”. (Catarrhine primates are old world monkeys and great apes, including humans.)
Here are some choice quotes from the paper on this point—all emphasis added:
"We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates . This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee. Our Southern analysis shows that human and orangutan completely lack PTERV1 sequence (see Figure 2A). If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely."
"While it is clear that this particular class of endogenous retroviruses shares a common origin, the retroviral phylogeny is inconsistent with the generally accepted primate species tree based on molecular data"
"the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor."
"This tree topology suggests a polyphyletic origin with at least three groups of Old World virus being distinguished."
"Our data support a model where ancestral chimpanzee and gorilla species were infected independently and contemporaneously by an exogenous source of gammaretrovirus 3–4 million years ago."
It seems incredibly clear that there are PTERV insertions that don’t match the standard phylogeny (or nested hierarchy, if you will) of higher primates.
Of course the paper doesn’t abandon common ancestry—but nobody claims it did. The paper cites independent insertion events in different lineages to explain why the data “is inconsistent with the generally accepted primate species tree based on molecular data”. That’s just fine! But the ENV blog’s author, Jonathan M. doesn’t claim they abandon common ancestry. He simply cites this paper to note that ERV distributions can be explained by “independent events”, rather than the usual explanation, as he quotes someone arguing ERVs show “humans and the other primates must share common ancestry”. Here’s what the ENV paper states:
Though there are other possible candidate hypotheses for this observation (such as incomplete lineage sorting), in the context of other indications of locus-specific site preference, this data is, at the very least, suggestive that these inserts may in fact be independent events.
So this refutes the accusations against this paper that I quoted above. It also renders the personal attacks against its author (“lies” not “honest”) totally inappropriate.
This thread should be useful for all of us to understand the dynamics of this debate: Critics constantly make accusations against ID proponents that they are both wrong and immoral/incompetent. At the very least, the personal “immoral/incompetent” stuff has no place in this debate—especially when it’s taking place among Christian brothers and sisters. Make your arguments, state your disagreements, but don’t attack people personally. (And we often find that the substance of the arguments against ID is also flawed, as we’ve seen here.)
Obviously this kind of nastiness all over blogs. We even see it right here, openly tolerated by BioLogos on its discussion board. But it goes much further:
But if theistic evolution’s leading scientists and scholars resort to this kind of unsavory rhetoric not just on their blogs, but also in their books, then we have a serious problem.
In my opinion, a massive apology is owed from Dennis Venema to the ID and creationist communities for his uncivil treatments of them in Adam and the Genome. This doesn't mean he can't disagree with them--if he disagrees then he can and should vigorously make his arguments! But the tone in the book is deeply damaging to this debate.
So I say this in a loving spirit: This is a great opportunity for Dr. Venema to do something good and praiseworthy before everyone. If Dr. Venema were to do apologize, it would hugely elevate this debate and do a lot to bring harmony among brothers and sisters who happen to disagree on questions of origins.
I have a feeling that ID proponents would lovingly accept Dr. Venema’s apology and gladly move on to more important things in this debate. For my little part, I know I would love the opportunity to do that.
You’ve seen the evidence. Your move.