Pseudogenes, Intelligent Design, and Kitzmiller - Part 2

This is a reply to both AMWolfe and Nuno. I am not at home at the moment however I still have access to an internet connection so I will reply to your objection with evidence that is freely found on the internet.
“Francis Collins (Biologos’ glorious founder) is a joke.” I have backed this up with evidence. Collins has never been able to intellectually defend his TE when presented outside the confines of TE scholarship. I have listed three occasions in which Collins has had to offer an intellectual defense of his faith and/or TE and in each case he failed badly. All of this incidences are found on the web. Are you suggesting that Collins in these cases did offer a cogent defense? Or that it is bad manners to point out the intellectual failures on TE and its proponents? Collins is a great scientist but he is not a theologian or philosopher and had failed to put forward a logical non-vacuous case for the compatibility of Neo-Darwinism and Christianity. Collins is correct when he states that TE “will not go out of style or be disproven by future scientific discoveries” (Lang. of God 210). But that is because Collins’ TE totally lacks content; it makes no claims and cannot be subjected to philosophical analysis. No argument can support it either (other than it cannot be disproved). If you think that Collins has put forward an argument for TE that he has defended against opposition than please provide details of a link and I will take it all back.

Darrell Falk. I must admit I am beginning to like Falk as he has, in recent years, become quite decent in his dealings with those Christians who are not TE. But sadly in the past he has been incredibly rude especially to Stephen Meyer. Do you remember when Francisco Ayala reviewed Meyers ‘Signature in the Cell’? In which Ayala addressed arguments that Meyer did not make and even got the title of Meyer’s book wrong. (http://biologos.org/blogs/archive/on-reading-the-cells-signature/). Falk presented Ayala as a great modulating influence on the science/religion dialogue and even linked to the 2006 ‘Beyond Belief’ conference and claimed that Ayaya kindly but forcefully admonished new atheists for their style. Actually what Ayala said at that conference in regard to religion was “There are six billion people in the world. If we think that we are going to persuade them to live a rational life based on scientific knowledge, we are not only dreaming — it is like believing in the fairy godmother. People need to find meaning and purpose in life I don’t think we want to take that away from them.”. Falk did offer Meyer a response but initially refused because Falk “felt his tone was insufficiently respectful of one of Biology’s living legends.” Which I am sure you would agree is just a ridiculous excuse.That Steve “was criticizing Ayala for doing a terrible job of something Ayala was never asked to do. He was not asked to review Signature in the Cell.”. This could be true but Falk did call initially call Ayala’s essay a review. That Steve had not done what we agreed he would do, which was to engage Ayala’s philosophical and theological arguments. Which I do not believe for one second as Meyer has always stressed that ID is a scientific theory and in any event how can you engage with someone’s Philosophical and theological arguments when they have failed to grasp even a basic idea of the book in question. The whole sorry story is here http://biologos.org/blogs/archive/on-not-reading-the-signature-stephen-c-meyer’s-response-to-francisco-ayala-part-1. Of course rather than apologize to Meyer, Falk went on the offence, attacking Meyer’s intellectual background and claiming that ID’s success and Meyer’s plausibility are due only to communication skills. The whole thing is here http://biologos.org/blogs/archive/on-reading-the-signature-a-response-to-stephen-meyer/. Falk and Meyer went on to exchange a number of essays which resulted in Falk concluding that Meyer understood the science well, was well read up on the cutting edge of research and that he considered ID as science. Falk had little choice, Meyer schooled him.

Karl Giberson. Giberson wrote in an article that the Discovery Institute wants taught in science classes include a 10,000-year-old earth, Noah’s Ark, and Adam and Eve:
“For starters, the “controversies” they want to teach don’t even exist. In their minds the possibility that the earth is 10,000 years old is an open question, even though geologists settled that one in the 18th century. They still think that Adam and Eve were real people and Noah may have rescued all the animals in the ark – claims settled in the 19th century.”
Discovery Institute Still Undermining Science | HuffPost Religion.
Giberson knows that this is not true; that is what makes him deliberately dishonest.
As for the photo shopped photo of a baby with a tail Giberson did apologize after it was conclusively proven that it was fake. The whole thing is here (Karl Giberson Apologizes for Photoshopped Image of Tailed Baby | Evolution News) with Giberson’s replies and quotes and other links to the debate with Stephen Meyer. But notice that Giberson goes on the offence and accuses DI of lies. How much more pathetic and unpleasant can a person be? As for the debate Giberson lost as he always does.
Francisco Ayala. I have already said a lot about him. However he continues to state that Behe claims that the eye is irreducibly complex or that ID argues against common descent. Of course many evolutionists state the same falsehoods. But what sets Ayala apart is that in addition to regurgitating false claims after the debate with William Lane Craig he claimed that he was set up that he had no idea that it was a debate but he was asked to give a lecture. This is just ludicrous, both Indiana University and Bradley Monton moderator confirmed that this was not the case. The debate is on the web and for a good atheist review Luke Muehlhauser.
I can only guess that Falk, Giberson, Ayala are all follow of Philip L Quinn’s advise on how to deal with ID and Creationism
“It sometimes happens that the best arguments one can give in support of a view are not going to be effective and the most effective arguments one can give are not going to be good. After all, decision-makers are sometimes too busy to master complex arguments. Then, too, they can be prejudiced or even stupid. When one is aware that this is the situation – and I suspect this is rather common – then one confronts the philosopher’s dilemma.
One horn looks roughly like this. Convinced of the overall rightness of one’s position, one opts to present the effective bad argument. Each time one does this, one’s hands get a little bit dirtier. At first one is painfully sensitive to even small compromises that one knows to be violations of one’s intellectual integrity, but gradually numbness of conscience sets in. At last, when presenting the effective bad argument has become easy and habitual – second nature, as it were – one’s hands have become dirty beyond all cleansing and one suffers from a thoroughgoing corruption of mind.
The other horn looks roughly like this. Concerned to preserve one’s integrity at all costs, one resolves never to present the effective bad argument. One always presents the best argument one can for the position one thinks most nearly right, and one’s hands remain clean. But frequently these good arguments fail to persuade or carry the day, and gradually one’s credibility and effectiveness wane. At last, when one has an established track record of failure, the decision-makers conclude that one is of no use to them, and one is unceremoniously cast aside.
Though it should be obvious that I have been exaggerating a bit for rhetorical effect, I think the hard choice between corruption and ineffectuality is sometimes real enough. That is the dilemma! Is there a way between its horns? Perhaps. My colleague, Dan Brock, suggests that academic philosophers should only get involved in the policy-making arena on a temporary, short-term basis. Maybe this is a way in which we could manage to have our cake and eat it too. For a short period one might engage in giving bad effective arguments without being thoroughly corrupted. Then one could retreat back to the academy to wash one’s moderately soiled hands.
After having one’s intellectual integrity restored and reinforced, one might then be ready to repeat the cycle.
The application of what I have been saying to the creationist controversy is straightforward. It seems to me that the attempts by creationists to foist their particular brand of dreadful science on public school curricula are pernicious. We should resist such attempts and resist them effectively in the political realm. But some of the creationists who are making such attempts are, to put it not too harshly, shysters. So there may well be circumstances in which only the bad effective argument will work against them in the political or legal arenas. If there are, then I think, though I come to this conclusion reluctantly, it is morally permissible for us to use the bad effective argument, provided we continue to have qualms of conscience about getting our hands soiled. But I also believe we must be very careful not to allow ourselves to slide all the way down the slippery slope to intellectual corruption. Perhaps, if we divide up the labor so that no one among us has to resort to the bad effective argument too frequently, we can succeed in resisting effectively without paying too high a price in terms of moral corruption.” But Is It Science 397-399
In other words lie.

Biologos (TE) never criticises atheism; never critically examines science; never criticizes the atheist stance of many modern scientific organizations. It seems to regard God and theology in a non-realist manner that can be dictated too, and even insulted by the scientific authorities. In other words science is factual; Christianity, God, the Resurrection are a set of warm fuzzy feeling that are strictly false as statements of reality. Its targets are only Christians who fail to accept the full Neo-Darwinian paradigm. Biologos is as much a political group as an academic one trying to create a world in which religious faith has the same content as a preference for tea over coffee.

All I mean is that you need both differences and similarities to show common ancestry.

Perhaps we would. I’m not claiming large-scale genome organization is good evidence for common ancestry; I’m responding to the claim that it’s evidence against common ancestry. It’s not. To the extent it supports anything, it supports common ancestry.

I’m afraid this argument doesn’t make sense to me. Normally, if you have two independent lines of evidence for a conclusion, then your confidence in that conclusion is strengthened. That’s what’s going on here. There’s nothing in a creationist view that would suggest that we should see a tree-like arrangement among living things, and yet we do. This makes it good evidence for common descent. When we see virtually the same tree-like arrangement in DNA – especially in DNA that has no function, or where similarity in function has no relationship to the similarity in sequence – then it is even more powerful evidence for common descent.

Sadly in this continuation of your earlier rant you never apologize for using a crass and offensive term for the female genitalia to refer to a brother in Christ.

Honestly it makes me feel kind of nauseated that I actually skimmed your rant-part-deux and lost minutes of my life that I’ll never get back.

Please consider taking your civil discourse up a notch. You might actually convince people of some of your points, instead of making them want to vomit.

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Having looked at it, I don’t find anything amusing about it. If anything, I’d say Venema was too generous to the ENCDOE folks. Their press releases, at least, were really disingenuous and gave the impression that they’d showed that 80% of the human genome had a meaningful function. The actual estimate of meaningful function coming out of the project was more like 10%.

I have given a fuller account in my response to another poster.

There are two aspects to this from a creationist perspective. First that everything biological, will likely operate on similar principles… thus the similarities. Second, that as organisms are grouped, they will be grouped according to similarities… thus we have the plant kingdom and the animal kingdom, for example, a grouping, and yet a distinction, based on living organisms separated by the characteristics of locomotion primarily, but then further on other factors. Then the animal kingdom divided by air, water, and land, in general, but more specifically also by feet, fins, wings, or scales, hair, feathers. Thus we have a tree in the creationist perspective, on the basis of organization. This has always been there.

Evolution did not create the concept, is my point. It is not a good evidence for common descent, but it is good evidence for an organization of ideas and concepts, and evidence for an organization of similarities and differences.

As far as Dna that has no function… I do not think we are at a point where we can prove that to the extent that it is assumed. Thus this is not at this point in time a definitive argument.

This is meaningless. A probability is only relevant to future events. So you need to get your tenses right. The probability of a past even occurring again, is nil, because a past event cannot occur again, unless it becomes a new future event. The probability of something in the past having happened, is based and balanced against it not having happened. So something with a probability of one in a million, could still happen, but that does not change the probabilty to one, once it happens.

In the case of our existence, we are not arguing about the probability of our existence (there’s simply no point to it), but we are arguing about the probability of our existence happening in a particular way. That probability is based on all the possible ways that our existence could have happened, combined with all the possible ways that these same processes might have led to a different result, where we did not exist.

not true. because we now know that there is no such a tree that show hierarchy. this is because lgt and degeneration.

You mean like this:

or this:
http://biologos.org/blogs/jim-stump-faith-and-science-seeking-understanding/senior-scholar-jeff-schloss-reviews-faith-vs-fact-by-jerry-coyne-in-the-washington-post
or this:
http://biologos.org/blogs/deborah-haarsma-the-presidents-notebook/reflections-on-our-interview-with-bill-nye
or this:

or this:
http://biologos.org/resources/scholarly-article/scientific-fundamentalism-and-its-cultural-impact
or this:
http://biologos.org/blogs/archive/exposing-the-straw-men-of-new-atheism-part-3
or this:
http://biologos.org/blogs/archive/more-responses-to-hawkings-the-grand-design
or this:

I could go on. We have dozens of articles criticizing atheism in our archive. I suppose what you might mean here is, “BioLogos doesn’t criticize atheism in the way in which I think atheism should be criticized, or defend Christianity the way in which I think it should be defended.” But at least be honest about that.

How do you define this? If you mean that BioLogos doesn’t take a hard look at the state of scientific evidence, you’re just wrong. There are so many links for this in our archive that I wouldn’t know where to start. But I want you to clarify what you mean before I proceed.

Which organizations? What atheist stance? We’ve persistently criticized the materialistic tendency in many corners of modern science, and particularly the “new atheist” movement (see links above). This has gained us no friends among materialistic scientists like Jerry Coyne (he called one of our newest videos a “steaming pile of excrement”). Again, I suspect what you mean is that we don’t criticize certain organizations in the way in which you think they should be criticized.

This shows that you not only completely misunderstand our mission but also our perspective. Can you provide any evidence for this claim? I’ll provide evidence for my defense. Here’s three BioLogos articles defending the resurrection as a historical event (and there’s more where these come from):

http://biologos.org/blogs/archive/does-resurrection-contradict-science
http://biologos.org/blogs/ted-davis-reading-the-book-of-nature/motivated-belief-john-polkinghorne-on-the-resurrection-part-4
http://biologos.org/blogs/jim-stump-faith-and-science-seeking-understanding/n-t-wright-and-the-resurrection-reviewing-“surprised-by-scripture”-part-3

And here’s our belief statement: The Work of BioLogos - BioLogos. For reference, here’s the first five tenets:

We believe the Bible is the inspired and authoritative word of God. By the Holy Spirit it is the “living and active” means through which God speaks to the church today, bearing witness to God’s Son, Jesus, as the divine Logos, or Word of God. We believe that God also reveals himself in and through the natural world he created, which displays his glory, eternal power, and divine nature. Properly interpreted, Scripture and nature are complementary and faithful witnesses to their common Author. We believe that all people have sinned against God and are in need of salvation. We believe in the historical incarnation of Jesus Christ as fully God and fully man. We believe in the historical death and resurrection of Jesus Christ, by which we are saved and reconciled to God. We believe that God is directly involved in the lives of people today through acts of redemption, personal transformation, and answers to prayer.

Does this really sound to you like Christianity is just “warm, fuzzy feelings” to us?

If you want to make a legitimate critique of BioLogos here, so be it. Many people have done so here. But making broad, evidence-less claims is not that.

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I appreciate that your follow-up comment consciously avoids the kinds of flat-out insults found in your original comments, but since your follow-up comment is anything but a retraction, I’ll assume that your insults and accusations still stand. From what I can see, your follow-up comment is a list of one-sided exposés of some sordid interpersonal politics that couldn’t be less connected with the scientific issues at stake. That’s fine, and I’m sure I’d probably seriously look into each accusation if these were personal friends of mine. Two reasons why it just isn’t worth it: (1) They are not and they can probably defend themselves if you want to get in touch with them and lovingly reprove them on each point that you feel discredits their integrity (2) As made clear by Brad below; your statements about Biologos itself are so extraordinarily off-base, counterfactual, and unfair, that I can’t imagine why your statements about anyone else need to be taken particularly seriously. Taking your critique of Biologos as a measure of what to expect for your other accusations, it is hardly worth even clicking on your links, let alone bothering to get some context for your points, and I’m sorry to say this, since it is clear that you put a lot of effort into trying to support your perspective. But again, thanks for toning it down. I’m curious to see how you respond to Brad’s comment.

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Brad,
I don’t consider any of the above criticism of atheist. They all just offer well expressed views of alternative beliefs. They all seem to be factually accurate and true. As you know, atheism is a belief that can’t be proven or disproven. And atheism has nothing to do with science or scientific research. Everyone is born atheist and then lives their life as 99% atheist as they don’t believe in any of the 10,000 or so gods postulated by human societies over the past 40,000 years except their own. Some believe in their own personal God, usually something along the lines as their parent’s God but remain unbelieving in all other gods. Others believe in one less god than you do. These statements are as true today as they were true 2000 years old. Only difference now is that in most countries of the world you are free not to believe in the State mandated God. Biologos is doing a good job of showing that whatever your beliefs are, you can understand and appreciate the marvels of modern scientific discoveries to live meaningful and purposeful lives.

Thanks for your helpful comments, Brad. Also, thanks to Steve - great to see you here. Folks, you’d do well to listen to Steve: he knows his stuff.

On the suggestion that I hide behind a computer - if that’s the case, the BioLogos forums are a poor place to do that! We have a very open and welcoming policy for commenters, and I value that very highly. We welcome critical, supportive and indifferent voices alike.

Also, the door is always open for folks like Craig or Poythress to comment or critique what I write about their work. I’d welcome the exchange. While I disagree with their scholarship, for the reasons I’ve given, they are my brothers in Christ first and foremost. If they’d like to take issue with my critiques I’m sure they would do so in a thoughtful way, and I’d be happy to reciprocate.

Years ago, I tried to register to comment at the ID blog Uncommon Descent. I registered using my real name, and my real university email address (which has my name in full). My registration was not approved. It seems I wasn’t welcome there. The Discovery Institute, obviously, doesn’t even allow comments at all. I’ve long thought that the strength of a position on the Christian origins spectrum is proportional to one’s willingness to allow commenters of all stripes.

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Brad is there any point in posting a reply? Or will you delete if it is not significantly aligned to the beliefs and mission of Biologos?

@MATT I deleted one of your posts that was full of insults. Other than that, every single one of your posts is still up. If you’re interested in making a thoughtful reply, go for it.

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Whoops. Look at [deleted] on Wikipedia and the British use of the word (a person who is obnoxious or stupid). I completely understand your outrage - I would never use language like that.

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It’s not true for bacteria, but it’s very much true for vertebrates, and for most animals. Bacteria undergo lots of horizontal gene transfer, while vertebrates have very little. Vertebrates, not surprisingly, therefore yield very good, consistent phylogenetic trees when their DNA is analyzed.

I took another look at GULO, by the way, to see if some common mechanism really could explain the exons that were lost in both humans and guinea pigs. Your argument was that humans lost 7 out of 12 exons from the gene, and that it was unlikely that the exons guinea pigs happened to lose 2 and a half of the same exons by chance (exons 1, 5 and part of 6). Instead, they must have undergone similar deletions because they had similar genomes.

So what does the sequence actually look like when you compare the two? Conveniently, a pairwise alignment of the human and mouse genome is available online, as is an alignment of guinea pig vs mouse (yay, Jim Kent and UCSC). Since mouse has a functioning copy of the GULO gene, it provide a reference copy of the gene that has all of the exons intact. Here’s what the first half of the gene looks like:

In the plot, the x axis shows the position in the mouse chromosome and the y axis the equivalent position in the corresponding guinea pig chromosome. Blue segments show where the two still have similar DNA; where there is a gap, there has been an insertion or deletion in one of the two species. The green segments above that show the same thing for the human chromosome – the segments where it resembles the mouse gene. Along the bottom, the red blocks show where the GULO exons occur in the mouse. (They are numbered right to left because the gene lies on the reverse DNA strand.)

The first thing to note is that none of the genomes are very similar to one another, and that there are numerous insertions/deletions throughout the gene. Also, there is no sign that similar deletions are occurring at the same places. Exon 6 is completely missing from the human copy of the gene because a substantial deletion has taken out the entire region, while the guinea pig exon has been clipped by a different deletion.

Things are different in the case of the other two exons in question (exons 1 and 5): it turns out in both cases that one of the two species isn’t even missing the exon. Exon 1 is still present in guinea pigs, while exon 5 is still present in humans. I’m surprised that exon 5 was listed as missing in humans, since the sequence there isn’t that different from mouse. Here are the two lined up:

Exon 1 is much more heavily altered by mutation, probably because it’s almost all noncoding, and therefore mostly not constrained by purifying selection even for functioning copies of the gene. Here is that stretch of the gene in mouse and guinea pig:

You can sort of still see the resemblance, but it’s only because it’s part of a large block of similarity between gp and mouse that we can we sure they come from a common original state. For both of these exons, the matching sequence in the other species was completely removed by large deletions, a completely different mutation process.

Based on the actual sequence comparison, then, the argument is plainly wrong that humans and guinea pigs have lost overlapping exons because of common mutational processes in the two species.

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@BradKramer,

Is there a way I can recommend this comment as a candidate for its own blog post? There may be some need to boil down the prior comment thread with DCS (and, long ago, me) so people have some background, but when somebody puts so much effort into a clear exposition of something that really contributes to understanding why data doesn’t fit a YEC explanation, it’d be a shame to see it buried so deep in the comments section.

Just my $0.02.

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Despite my surprise, I see that doing the obvious, simplest comparison between mouse and human indeed fails to find exon 5 in humans. That comparison is a search using the program BLAST, with default parameters. (Anyone can try it for themselves. Go to Transcript: ENSMUST00000059970.9 (Gulo-201) - Exons - Mus_musculus - Ensembl genome browser 111
where you should see displayed the mouse exons for GULO. Highlighting some of the sequence should cause a box to pop up, offering to BLAST the sequence. Pain-free bioinformatics.)

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hey again glipsnot.

not according to those scientists:

“Charles Darwin’s “tree of life”, which shows how species are related through evolutionary history, is wrong and needs to be replaced, according to leading scientists.”

“We have no evidence at all that the tree of life is a reality,” Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, told New Scientist magazine."-

and its not just about bacteria:

“Last year, scientists at the University of Texas at Arlington found a strange chunk of DNA in the genetic make-up of eight animals, including the mouse, rat and the African clawed frog. The same chunk is missing from chickens, elephants and humans, suggesting it must have become wedged into the genomes of some animals by crossbreeding.”

not according to this paper:

http://www.jbc.org/content/267/30/21967.long

you can see that exon 1 is missing from the guina pig and rat comparison (fig 3). so you are claiming that you found what 2 scientific papers doesnt found? it will be interesting.

even if its true i can give you another examples. it doesnt change the fact that shared mystake can be found without a commondescent. so shared mystakes isnt evidence for a commondescent.

For completeness, here is the alignment of guinea pig and several primates for the entire mouse GULO gene.

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