Monday, September 3, 2007

Challenges for Uncommon Descent

Added: Case #1 challenge met! Good for scordova.
Added: Case #2 resolved* under threat.
Edited: Fixed the link to the Cell article.

Having been banned at Uncommon Descent, I can only witness its self-destruction from afar.

Like one watching a nuclear test with sunglasses, I witnessed their humiliating hoax letter "from" Baylor's president and its attempted suppression. Nobody should be angrier about this than Robert Marks. Here's a guy who's trying to help Dembski out, and Dembski's group -- if "Botnik" is not Dembski in disguise -- responds by insulting his current employer. Dembski's final sentence in his suppression note is hilarious:
I hope Baylor and President Lilley take its removal as a gesture of goodwill on the part of UD as they reconsider what to do about Robert Marks and his Evolutionary Informatics Lab.
With friends like that, eh Robert Marks?

Anyway. The fiasco has been duly mocked by science bloggers (denialism, Afarensis) and the whole incident has been archived for future mockery at The Panda's Thumb. An inadvertent effect of this mockery is that it may raise UD's lousy numbers. (I have no readership, of course, but who am I next to the mighty Dembski?)

But that's not the point of this post. My goal is to answer a simple question: will UD writers retract anything that is shown to be wrong, and not just, as with the Baylor fiasco, stupid and juvenile?

Two cases:

Case 1: RESOLVED! Before he went underground, scordova at UD accused ERV of purposely misleading her readers, a charge that is easily disproven. He has been asked to retract this poisonous and false charge on ERV's blog, and I have asked other UD readers to disclaim it on UD. So far, no luck. So: will anybody at UD have the dignity to say that scordova was wrong, indeed scandalously so, when he wrote this?
But she knows up front that I will call her on an equivocaqtion that was in the minds of some PT’ers when she made an appeal to HIV-2 to make it seem that HIV-1 developed a new Vpu gene after it entered humans. (Emphasis added)
Later in the thread, I responded as follows:
Sal wrote that ERV "made an appeal to HIV-2 to make it seem that HIV-1 developed a new Vpu gene after it entered humans."

Absolutely, utterly wrong. In the original post, ERV wrote, "Of the five major phylogenetic groups of SIV, Vpu is only found in one group-- Chimpanzee SIV (SIVcpz) and its descendants—including HIV-1."

Can you read that? A form of Vpu is found in Chimpanzee SIV, of which HIV-1 is a descendant. Straight up. Retract and apologize.
scordova accused ERV of deliberately deceiving her readers, a charge that has been shown to be without merit. Will someone -- anyone -- at Uncommon Descent have the decency to disclaim this charge? You don't have to believe anything she wrote, but isn't anyone going to step up and say this is BS?

Case 2: RESOLVED* UD commenter Joe G wrote: "Does anyone even know what gene or genes is responsible for the vision system? No."

I refer to the following from Science Daily, 2001: Comprehensive Set Of Vision Genes Discovered: Identification Could Help In Diagnosing And Treating Blinding Diseases. This article begins, "Harvard Medical School researchers have discovered nearly all the genes responsible for vision, which could help in diagnosing and treating blinding diseases."

The full text of the original research (from November 30 2001 Cell) is available here.

Will anybody at UD say, "actually, yes." I've written to Joe G about this, so he knows. Will he correct himself? Wait and see.

Props to oldmanintheskydidntdoit for the reference in Case 2.

*Resolution reached on threat of violence.

61 comments:

SPARC said...

Do you really beleave that Sal would retract anything? He may be quiet for some time. However, I am not sure if he isn't currently working on his own EXPELLED myth. Dembski already presents the end of his last affair with Baylors as being EXPELLED (or do you think this is just another of his PARODIES?). Maybe the two of them finally make it into the EXPELLED movie.

Joe G said...

Either Hermagoras is extremely stupid or just plain ole dishonest.

There isn't anything in either article which demonstrates we know the answer to my question:

"Does anyone even know what gene or genes is responsible for the vision system? No."

The "No" still stands.

I was NOT asking if we knew how the vision system worked. I was not asking for info on some of the primary causes of vision failure.

Also I can't believe how much is being made from a parody.

I take it this is all you have when you don't have any scientific data to make your case.

blipey said...

JoeG to the rescue! I haven't laughed so hard for a minute or two (I was just over at Ftk's newly reopened site.).

So, Joe, it is your opinion that a study that has discovered all of the genes for rods and cones has discovered no genes relating to vision?

Wow.

If you are referring to the original work in Cell, have you read it?

blipey said...

Oh, Joe. Please reconcile the following:

1. the researchers identified approximately 300 photoreceptor genes

and

2. Does anyone even know what gene or genes is responsible for the vision system? No.

Thanks.

Joe G said...

So, Joe, it is your opinion that a study that has discovered all of the genes for rods and cones has discovered no genes relating to vision?

No, that is not my opinion nor does it address my question.

The vision system consists of more than photoreceptor genes.

If you are referring to the original work in Cell, have you read it?

Yes I read it.

The research paper wasn't even interested in answering my question. That was not its focus.

Do you even know what a vision system entails? For humans it entails much more than what the paper talked about.

Also "responsible for" means more than "allows it to work".

blipey said...

Juliet W.L. Parry, Karen L. Carleton, Tyrone Spady, Aba Carboo, David M. Hunt, and James K. Bowmaker
Mix and Match Color Vision: Tuning Spectral Sensitivity by Differential Opsin Gene Expression in Lake Malawi Cichlids
Current Biology 2005 15: 1734-1739. [Summary] [Full Text]
Joseph M. Bateman and Helen McNeill
Seeing in Color — warts and All
Developmental Cell 2005 9: 441-442. [Summary] [Full Text]
Tamara Mikeladze-Dvali, Mathias F. Wernet, Daniela Pistillo, Esteban O. Mazzoni, Aurelio A. Teleman, Ya-Wen Chen, Stephen Cohen, and Claude Desplan
The Growth Regulators warts/lats and melted Interact in a Bistable Loop to Specify Opposite Fates in Drosophila R8 Photoreceptors
Cell 2005 122: 775-787. [Summary] [Full Text]
Shaun P. Collin, Maree A. Knight, Wayne L. Davies, Ian C. Potter, David M. Hunt, and Ann E.O. Trezise
Ancient colour vision: multiple opsin genes in the ancestral vertebrates
Current Biology 2003 13: R864-R865. [Full Text]
Eloísa Herrera, Lucia Brown, Jun Aruga, Rivka A. Rachel, Gül Dolen, Katsuhiko Mikoshiba, Stephen Brown, and Carol A. Mason
Zic2 Patterns Binocular Vision by Specifying the Uncrossed Retinal Projection
Cell 2003 114: 545-557. [Summary] [Full Text]
Adam Claridge-Chang, Herman Wijnen, Felix Naef, Catharine Boothroyd, Nikolaus Rajewsky, and Michael W. Young
Circadian Regulation of Gene Expression Systems in the Drosophila Head
Neuron 2001 32: 657-671. [Summary] [Full Text]
Roderick A Corriveau, Gene S Huh, and Carla J Shatz
Regulation of Class I MHC Gene Expression in the Developing and Mature CNS by Neural Activity
Neuron 1998 21: 505-520. [Summary] [Full Text]
Jairaj K Acharya, Kees Jalink, Robert W Hardy, Volker Hartenstein, and Charles S Zuker
InsP3Receptor Is Essential for Growth and Differentiation but Not for Vision in Drosophila
Neuron 1997 18: 881-887. [Summary] [Full Text]
Martin J. Tovée
Colour Vision: Dalton's eyes and monkey genes
Current Biology 1995 5: 583-586. [Summary] [Full Text]

try reading here

I know, I know. One of two things is true here.

1. You've already read all these papers (and probably embarrassed the authors in public debate).

2. Without reading them you know that they have nothing to do with vision genes (a la Behe).

SHOW THE WORK! SHOW THE WORK! SHOW THE WORK!

Hermagoras said...

Joe,

You read the whole Cell article? Really? But my link didn't work until I fixed it a moment ago.

Ah well. I thought you were going to go there. So by visual system you don't just mean the eye, you mean things like the LGN and the visual cortex and their relation. But on the other hand, you were responding to a question about the eye. So pretending that the genes responsible for the eye's significant contribution to vision are irrelevant is simply shifting the goalposts.

What would satisfy you? Every gene for the eye, the LGN, the optic nerve, and the visual cortex?

Let me remind you of the abstract:

"To identify the full set of genes expressed by mammalian rods, we conducted serial analysis of gene expression (SAGE) by using libraries generated from mature and developing mouse retina. We identified 264 uncharacterized genes that were specific to or highly enriched in rods. Nearly half of all cloned human retinal disease genes are selectively expressed in rod photoreceptors. In silico mapping of the human orthologs of genes identified in our screen revealed that 86 map within intervals containing uncloned retinal disease genes, representing 37 different loci. We expect these data will allow identification of many disease genes, and that this approach may be useful for cloning genes involved in classes of disease where cell type-specific expression of disease genes is observed."

Nope. No visual system genes here.

blipey said...

Damn! Hermagoras!

Don't you know that JoeG has read EVERY journal article EVER PUBLISHED, by anyone, anywhere.

He has also personally debated and embarrassed every scientist who has ever lived and ever will live, which he can do because of the time machine he invented. This is why he has an ultra-top-secret, trans-Plutonian, Velikovsky Clearance.

Joe G said...

You guys hacve serious issues and need professional help.

"Does anyone even know what gene or genes is responsible for the vision system?

That means the ENTIRE VISION SYSTEM. Including the type of eyes we have- as opposed to having chimp-eyes (for example).


I specifically said "vision system" because an "eye" or "eyes" are useless without the entire system.

Perhaps you should ask for clarification BEFORE you run around like a chicken with its head cut off.

Don't blame me because you don't understand the question.

What would satisfy you? Every gene for the eye, the LGN, the optic nerve, and the visual cortex?

Everything. Where is the info for the type of eye?

For example substitute a PAX6 from a mouse with a fly and the fly develops fly-eyes. The PAX gene is just a switch.

BTW- the link you posted on my blog works fine.

I downloaded the article. It only refers to some of the cells in the retina.

Joe G said...

I never said nor implied that we didn't know anything about the vision system.

Hermagoras said...

So the "even" was just a bit of fluff? We know a lot about the visual system, but we don't "even" know everything about its genetics? What a bullshitter you are.

blipey said...

But you are implying that it will be impossible for us to ever know everything about it.

ID must be true because you guys don't know everything about the vision system. And it is clear that since something new is being discovered every day, we will never know very much about the vision system. Huh???

Ridiculous.

Joe G said...

But you are implying that it will be impossible for us to ever know everything about it.

I made no such implication.

Perhaps your twisted little mind inferred that is what I was saying, but that is another story.

Hermagoras said...

But until we DO know everything -- absolutely everything -- about it, then "Does anyone even know what gene or genes is responsible for the vision system? No." Right Joe? Until we know everyhing?

Hermagoras said...

Joe, you have underwhelmed me. Scordova is more capable of being shamed into honesty than you are. That's saying something.

blipey said...

But when we know everything, the question will be wrong.

Joe G said...

to clowny-

Did you read those articles you presented?

blipey said...

Of course not. That wasn't the point. The point was that you either:

1. Will claim to have read them all.
2. Will claim that they are wrong, even if "1" is not true.

Thanks for forgetting your own MO.

Joe G said...

Again the vision system is much more than the cells in the retina.

I cannot help it if you choose to interpret something I posted into something I didn't say.



And when we know everything ID will be confirmed.

blipey said...

"When we know everything, ID will be confirmed."

That's how science works!!! Shit up a stick, I never knew that.

We don't have to have predictions, or experiments, or anything!

We'll just wait till we know everything and then claim victory!

Man, this science stuff is easier than I thought.

Joe G said...

Wrong again clowny.

I only pass judgement on an article AFTER I have read it.

However, you, like most evolutionitwits, always post an artcle without reading it. You go just by the title.

Hermagoras said...

Joe wrote,

"And when we know everything ID will be confirmed."

Joe, I think this is what you're looking for:

"Now we see but a poor reflection as in a mirror; then we shall see face to face. Now I know in part; then I shall know fully, even as I am fully known." 1 Cor 13:12.

Joe G said...

We don't have to have predictions, or experiments, or anything!

That's a good thing for the theory of evolution!

No predictions and definitely no experiments to demonstrate anything that is being debated is even possible.

Joe G said...

Joe, I think this is what you're looking for:

Don't think. It is harmful to those around you.

Joe G said...

"When we know everything, ID will be confirmed."

That's how science works!!!

Yes, science is an accumulation of knowledge.

First graders know that clowny...

Hermagoras said...

Joe, is it really your contention that until we know everything about the visual system's genetics, the following statement will still be true?

"Does anyone even know what gene or genes is responsible for the vision system? No."

I'm just trying to see how far you're willing to stick your head up your ass in order to avoid taking back such a stupid statement.

blipey said...

However, you, like most evolutionitwits, always post an artcle without reading it. You go just by the title.

The point was not that I have or have not read the papers. The point is that by the abstracts, they all deal with genes that are integral to the vision system. Does any one paper deal with the entire vision system? Probably not, I haven't read them. The point is that there is ongoing, FRUITFUL work into the vision system and that a very large part of genomic basis for this system has been identified. The flavor of this body of work seems to run counter to your claim that nobody knows anything about the vision system and that it will be practically impossible for an evolutionary scientist to learn anything about it.

On your claim that biologists don't cite, you can't be serious? Almost every discussion on AtBC and PT, Afarensis, etc cites primary literature and then discusses it.

Those people are not DaveScot, who once cited a paper entitled "Gravity: the weakest force in the universe." to prove that gravity was the strongest force in the universe. Or Dembski, who just Googles "Intelligent Design" and posts evolutionary articles claiming that they are pro-ID.

Ah, good days indeed.

Joe G said...

Why can't you just admit that you misunderstood what I posted?

Or is your head to far up your ass to do so?

Hermagoras said...

"Why can't you just admit that you misunderstood what I posted?"

I didn't misunderstand. Anyone reading the context would understand it to mean, "we don't EVEN know the genes for the visual system," or in other words, that we don't know shit about the genetics of the visual system. It was a clear appeal to how little we know about the genes of the visual system. The entire point of your post was to suggest that we are ignorant of the genes of the visual system. At the time, the discussion was limited to the eye. When I point out that a paper identifying "the full set of genes expressed by mammalian rods" was published six years ago, you say "well, we don't know everything about the visual system's genes, so I'm still right." But nobody reading your original post would have seen that as your point. So, thanks for shifting the goalposts, and for continuing not to rise to the level of a scordova.

blipey said...

Joe, Joe, Joe. You're doing it again. Hermagoras has previously used the "head up ass" marker. You need to make it your own, not just parrot it.

Take your cues from someone other than the UD crowd.

New information in every post, please.

Joe G said...

The context:

Stuart Harris said:
For example, one can come up with many plausible Darwinian explanations for the evolution of the vertebrate eye given the starting point of a light sensitive cell.

I said:
Can that same person verify that explanation with actual scientific data? No.

Does anyone even know what gene or genes is responsible for the vision system? No.



It is very telling that hemogoras completely avoided the first question.

And knowing bits and pieces is like saying I knoiw how the computer is designed because I know where resistors, transistors and ICs are made.

blipey said...

So it is your position that knowing something about the genomic basis of parts of the vision system provides no data?

blipey said...

This is really the exact same "KNOW EVERYTHING or NOTHING" argument, Joe. The first paragraph adds nothing to context of the discussion.

Joe G said...

I didn't misunderstand. Anyone reading the context would understand it to mean, "we don't EVEN know the genes for the visual system,"

You did misunderstand because only an imbecile would chop it up that way.

"Does anyone even know what gene or genes is responsible for the vision system?

RESPONSIBLE FOR.

Are you that stupid that you don't understand the meaning of "responsible for"?

Taken in context it would have to deal with its evolution.

or in other words, that we don't know shit about the genetics of the visual system.

I did not say nor imply such a thing.

Your inference skills suck and you want to blame me.

That clowny agrees with you supports me.

At the time, the discussion was limited to the eye.

It wasn't limited to the eye and you were not even part of it.

IOW you put your nose where it doesn't belong and it got smacked.

Joe G said...

So it is your position that knowing something about the genomic basis of parts of the vision system provides no data?

That's not my position.

Is it your position to be as stupid as possible?

Joe G said...

clowny-

You never add anything to the content of a discussion.

You are a pimple on the ass of progress.

And the bottom-line is other people don't get to tell me what I was talking about.

There is a reason you guys are banned from UD...

Hermagoras said...

"New information in every post, please."

Impossible. As readers of NFL know, there's no such thing as new information.

Joe G said...

As readers of NFL know, there's no such thing as new information.

It doesn't say that in NFL.

But I take it your aren't misrepresenting it either...

Hermagoras said...

"There is a reason you guys are banned from UD..."

Certainly there is. For example, here's the reason Dr. Dr. Dembski gave at the time (mistakes in original):

"The arguments from obscrue, irrelevant, and nonexistent reference are relevant to this discussion."

Pissing off Dr. Dr. Dembski so much he can't write a coherent sentence: Priceless.

Hermagoras said...

Joe G said,

As readers of NFL know, there's no such thing as new information.

It doesn't say that in NFL.

But I take it your aren't misrepresenting it either...


Whoops! My bad. New CSI requires intelligence. Which explains the repetitiveness of your posts. I'm not sure how to explain the lack of humor.

Joe G said...

Stuart Harris said:
For example, one can come up with many plausible Darwinian explanations for the evolution of the vertebrate eye given the starting point of a light sensitive cell.

I said:
Can that same person verify that explanation with actual scientific data? No.

Does anyone even know what gene or genes is responsible for the vision system? No.


"Responsible for", in context, would mean "the cause of". As in what evolutionary steps could possibly bring about the evolution of the vision system.

No body knows.

And despite what clowny thinks the first paragraph adds context. Which is something clowny wants to avoid.

Joe G said...

New CSI requires intelligence.

That's not in NFL either.

Don't worry. You just don't get it and probably never will.

Hermagoras said...

Joe G said,

New CSI requires intelligence.

That's not in NFL either.

Don't worry. You just don't get it and probably never will.


Holy shit, Joe, I know the book well enough to riff on it. Apparently better than you:

NFL, p. 161: "[O]rdinary experience also tells us that complex specified information originates from intelligence."

NFL, p. 163: "The Law of Conservation of Information is not saying that natural causes in tandem with intelligent causes cannot generate CSI but that natural causes apart from intelligent causes cannot generate CSI."

NFL, p. 164: "To explain an instance of CSI requires either a direct appeal to an intelligent agent who via a cognitive act originated the CSI in question, or locating an antecedent instance of CSI that contains at least as much CSI as we started with."

"Intelligent causes generate CSI whereas natural causes transmit preexisting CSI (and usually imperfectly)."

"With CSI the information problem never goes away short of locating the intelligence that originates the CSI."

Etc.

Hermagoras said...

From the index to NFL, page 392, the term "Intelligence" has a number of subcategories. Between "machine" and "presupposes choice," we find:

only known source of CSI, 164, 207, 371

So, Joe. Are you still contending that the notion that "new intelligence requires CSI" is not in NFL?

Joe, let me write your response for you:

"Hermagoras, are you this stupid? By 'intelligence,' I didn't mean 'intelligence.' And by 'CSI' I was clearly referring to the TV show (the Las Vegas one, where we can test the explanatory filter on a saline boob.)"

Joe G. Still not as dignified as scordova.

Zachriel said...

Hermagoras: "Holy shit, Joe, I know the book well enough to riff on it. Apparently better than you:"

Let's add an eloquent paraphrase from ERV's sarcastic mouth.

Im looking at a copy of 'NFL' right now. Would you like to read it out loud together? "Experience also tells us that complex specified information originates from intelligence".

blipey said...

What, Joe?

You couldn't be wrong about the NFL stuff, could you? No way.

What's the reconciliation now?

To ignore it?

Great.

Hermagoras said...

Interestingly, Joe even says the same thing on his own blog, in his hamhanded, poorly written way:

". . . every experience and observation says CSI only comes from an intelligent source, that is a source which can create counterflow. Therefore with that experience and observational data in hand we would predict that every time we observed CSI and didn't know the cause an intelligent agency will be found responsible.

So by finding CSI arising without agency involvement a central tenet of ID is removed and ID falls."

Now, I don't accept this view of CSI. Indeed, I find the whole concept incoherent. But Joe clearly agrees that according to ID, new CSI requires intelligence. Until he needs to say it doesn't.

I think I can't convince Joe that Dembski's concepts are equivocal because Joe has no need for concepts to be consistent.

Steverino said...

"Does anyone even know what gene or genes is responsible for the vision system? No."

Joe, the question, in the context of your phrasing, has been answered. So, you are just wrong.

Doppelganger said...

Classic Joe G.....

Hilarious. I guess that is what happens when you get all your information on a subject from advocacy videos and propaganda books.

R0b said...

And the bottom-line is other people don't get to tell me what I was talking about.

Since you obviously don't know what you're talking about, how will you ever know unless someone tells you?

Does anyone even know what gene or genes is responsible for the vision system? No.

"Responsible for", in context, would mean "the cause of". As in what evolutionary steps could possibly bring about the evolution of the vision system.


So you think that a certain gene or set of genes caused the evolution of the vision system? You would have us believe that you don't understand the difference between development, which is dictated by genes, and evolution, in which the environment is a huge factor? You should have just conceded the question instead of digging deeper.

Speaking of which, you've got an awful lot of holes to dig yourself out of in this thread.

R0b said...

Hermagoras: So, Joe. Are you still contending that the notion that "new intelligence requires CSI" is not in NFL?

Joe, let me write your response for you:

"Hermagoras, are you this stupid? By 'intelligence,' I didn't mean 'intelligence.' And by 'CSI' I was clearly referring to the TV show (the Las Vegas one, where we can test the explanatory filter on a saline boob.)"


LoL. And by NFL he obviously meant the National Football League. There's no way he could be dumb enough to claim what he seemed to be claiming.

blipey said...

There's no way he could be dumb enough to claim what he seemed to be claiming.

Um. There is no basis for this statement.

Joe G said...

David Kellogg,

You have serious issues and need professional help.

"New CSI" is NOT the same as the origin of CSI.

See page 162 of NFL.

CSI is all about the ORIGIN of the complex specified information.

IOW the ORIGIN of CSI requires intelligence. New CSI can come about by rearranging existing CSI.

What is really funny is that Zachriel agrees with me but probably thinks he is correcting me.

You people are just too stupid to deal with.

c-ya (you know where to find me)

Hermagoras said...

Yes, "New," as in "novel," as in "natural causes never produce things de novo or ex nihilo" (NFL 162). Hence my considered use of the term "New." I read the passage pretty carefully and used "new" deliberately.

But no, I don't know where to find you. I don't know your real name, or where you are, nor am I concerned to try. As you have demonstrated on your blog, however, you know where to find me and have proudly displayed my name and institution like a hunting trophy. Hmm. How should I take this? You know who I am, but I don't know who you are. You have identified me by name and institution on your blog. This may give you a feeling of power over me.

Should I feel physically or otherwise threatened, Joe? Are you going to show up at my door? You say you're in New England; perhaps you're just around the corner. What possible reason other than intimidation could you have for pointing out that you know my name and institution?

Also, we both agree that I'm fat. That contributes to the argument how exactly?

blipey said...

See, Complex specified information is all about the origin of Complex Specified Information.

Didn't you ever learn how to define things?

Hermagoras said...

blipey,

I deleted your comment identifying Joe G. I'm not going to sink to his level, or have that on my blog.

R0b said...

"New CSI" is NOT the same as the origin of CSI.

Bravo, Joe, for equivocating in a way that none of us anticipated. Now if you can just make your attempted sleight of hand a little less transparent, you might have a chance at being taken seriously.

Do you know what de novo means?

Do you think that when Meyer refers to "new CSI that appeared with the Cambrian animals", he's talking about old CSI that's rearranged? Or is Meyer, like Hermagoras, unable to differentiate between "new" and "originate".

Do you know that "new" is an adjective and "originate" is a verb? BTW, have you figured out what a transitive verb is yet?

A Google search on "new csi" dembski returns 128 hits. How many of them are referring to rearranged old CSI? None. Apparently nobody but Joe can differentiate between "new" and "originate".

Hermagoras said...

I take it back! Uncle! Uncle!

blipey said...

Hermagoras:

apology on other thread. Won't happen again.

Hermagoras said...

I understand the emotions. But I'm not going to go there.

R0b said...

I'm waiting for Joe to tell us what idiots we are for not knowing that today is Opposite Day.