Pseudogenes, Intelligent Design, and Kitzmiller - Part 2

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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Nowhere does that article suggest that horizontal gene transfer is common in animals. As I said, it occurs but is not common. You can find a balanced (and later) assessment here. Relevant snippet: ‘The results suggest that “if we use the same yardstick to measure a variety of model organisms, it’s possible to say that mammalian genomes have also been subjected to low levels of HGT, although it happened only on very rare occasions at the early stages of evolution.’"

Read the paper. “On the other hand, regions corresponding to exons I and V were not identified in the guinea pig Lgulono-y-lactone oxidase gene homologue”, and “The regions corresponding to the rat GLO gene exons except for exons I and V were identified in the guinea pig gene, and their sequences were determined.” They didn’t show that exon 1 was missing: they failed to find exon 1. (They examined the sequence for exon 5 and showed that it wasn’t present, but did not do the same for exon 1.) Since they were searching for the gene by physically hybridizing the DNA, it would have been impossible for them to find exon 1, given how divergent the GP and mouse exons are.

As I said, I didn’t find anything. The finding was done by the comparative genomics folks at UC Santa Cruz. I just downloaded the files. They do their cross-species alignment using whole-genome sequence and the tool BLASTZ. That approach is dramatically more sensitive than the GP study (which was done 20+ years ago), and also more sensitive than the search that missed human exon 5, which used BLAST rather than BLASTZ.

Fine – let’s see the next example.

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true. i reffer to a different tree made by different (regular)genes, and not about lgt. we know that its very common that some genes tell different story. see this paper for example:

2)evolution cant explain how this lgt happan in animals. so even one event is a problem to the evolution senario.

fair enough. but still- why this result have not publish in a peer review article? why the new article from 2011 doesnt fix this? where is the peer review?

here is an example of 2 mutations without a commondescent:

and even in the gulo one rat share one base with chimp.

Sure, single-gene studies are noisy, but that is easily addressed by using more sequence. Incomplete lineage sorting means that closely spaced branches don’t actually have a unique tree, but that is expected and also easily dealt with. There are indeed real problems with ordering deep branches that are fairly close together: there simply isn’t enough information to determine the tree. But none of that changes the fact that DNA routinely produces reliable trees; it just means that there are well-known spots in the trees where the precise order is uncertain.

Sure it can (or rather, biology can – it’s not really the job of evolution). There are multiple plausible mechanisms for HGT in animals, several of which have been observed in intermediate states.

Because it’s trivial. Basically, no one cares. With whole-genome databases readily available, no one is going to go back and update all of the single-gene sequencing studies in the literature.

Which mutation do you mean? (It’s hardly surprising that the same mutation occurs independently in multiple lines, by the way. What we’re looking for is convergent mutations that happen more frequently than you would expect by chance.)

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there is a lot of problems with this method that we can discuss about. but the main point is that this tree isnt evidence for a commondescent more then a commondesginer.

can you give an explanation for lets say this one:

http://www.biolbull.org/content/227/3/300.abstract

about the uox pseudogene- i reffer to those mutations:

" One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications"-

and the mutation at codon 107:

“The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation”

Sure it is. Common designers routinely violate hierarchical trees. In fact, that’s an important component of intelligent design – any software engineer can tell you that good design involves reusing components across diverse applications.

That’s an interesting one. It will take me a while to dig out the sequence to look at it.

That’s not an interesting one. That a recurring mutation at a “CG” dinucleotide, better known as a CpG. That particular combination of nucleotides mutates to T at a very high rate (because the C in that pair is usually methylated, and methylated C spontaneously deaminates to thymine). They’re routinely discarded from many comparative analyses because recurrent mutations are so common at such sites. So multiple independent mutations at this site are not surprising. (Something I believe is mentioned in the paper somewhere.)

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true. but the same can be find in nature. unless you refer to a non-hierarchical tree. so what tree are you refer to?

i will wait.

its very interesting because now we have 2 share mutations without a commondescent. therefore a shared mutations cant be evidence for a commondescent.