Why English professor David Kellogg should stay out of scientific discussions
This also applies to secondclass who thinks that the scientific paper below tells us what genes are responsible for photoreceptors.
English professor David Kellogg seems to think the article refutes my claim that we do not know what is responsible for the vision system.
Comprehensive Analysis of Photoreceptor Gene Expression and the Identification of Candidate Retinal Disease Genes
For those who do not know, photoreceptors are cells (in the eye- the retina to be exact) that detect light.
The human eye has two types of photoreceptors- rods & cones. Rods do not discriminate among colors of light. Cones provide us with color vision.
With that said all the article is discussing is genes that are expressed in rods. Again rods are eukaryotic cells- cells with a nucleus- meaning they contain the same DNA that all other cells in your body contain in their nucleus. (red blood cells aren't really cells, they are "formed elements")
What the paper is discussing are the genes that are expressed in rods. That they are expressed in rods does not make them responsible for rods.
That distinction goes to the control genes- that is the genes that control and direct cellular differentiation.
IOW it appears that Kellogg, secondclass and a host of other anti-ID zealots do not have the first clue when it comes to biology.
English professor David Kellogg seems to think the article refutes my claim that we do not know what is responsible for the vision system.
Comprehensive Analysis of Photoreceptor Gene Expression and the Identification of Candidate Retinal Disease Genes
The functional breakdown of the genes selectively expressed in rods is shown in Figure 3. We saw a broad spectrum of functional categories of rod-enriched genes (see Figure 3 legend for selected examples and Supplemental Table S10 for a full list of genes). We saw a number of uncharacterized putative zinc finger transcription factors only expressed in rods, along with a number of other more broadly expressed transcription factors and coactivators, such as ERRβ2, Sox11, and All, which showed strong enrichment in rods. We observed several mammalian homologs of Drosophila genes, such as muscleblind and nemo-like kinase, which have been implicated in later stages of photoreceptor development (Begemann et al. 1997; Choi and Benzer 1994 and Zeidler et al. 1999). We observed many protein kinases and phosphatases, along with a TNF family ligand and several potassium and calcium channel subunits.
For those who do not know, photoreceptors are cells (in the eye- the retina to be exact) that detect light.
The human eye has two types of photoreceptors- rods & cones. Rods do not discriminate among colors of light. Cones provide us with color vision.
With that said all the article is discussing is genes that are expressed in rods. Again rods are eukaryotic cells- cells with a nucleus- meaning they contain the same DNA that all other cells in your body contain in their nucleus. (red blood cells aren't really cells, they are "formed elements")
What the paper is discussing are the genes that are expressed in rods. That they are expressed in rods does not make them responsible for rods.
That distinction goes to the control genes- that is the genes that control and direct cellular differentiation.
IOW it appears that Kellogg, secondclass and a host of other anti-ID zealots do not have the first clue when it comes to biology.
posted by Joe G @ 10:47 AM
18 Comments:
At 11:31 AM,
Hermagoras said…
Joe, I already cried Uncle days ago. Why the obsession?
At 11:56 AM,
Joe G said…
The obsession is all yours.
And because you started this I will stop when I think it is enough.
IOW this is part of my doing whatever it takes to shut you up.
I don't need to get physical with you. I can beat you up with knowledge.
That is always the best way to go- don't ya think?
At 11:57 AM,
Hermagoras said…
I have already mentioned that I accept your view of what you meant by your original comment. So I don't think you need to pursue that. But is the statement even as you meant it correct? Again, you wrote:
"Does anyone even know what gene or genes is responsible for the vision system? No."
If you're looking for control genes responsible for early eye evolution, Pax6 would be a major candidate, along with related genes Pax2 and PaxB (and probably some ancestral version of the latter). So if your original comment was meant as you claim -- which I have accepted -- then I still think we know a fair amount about the genes "responsible for the vision system."
See:
Franck Pichaud and Claude Desplan, "Pax genes and eye organogenesis,"
Current Opinion in Genetics & Development 12.4 (2002) 430-434.
Zbynek Kozmik, "Pax genes in eye development and evolution,"
Current Opinion in Genetics & Development 15.4 (2005) 430-438.
Zbynek Kozmik et al., "Role of Pax Genes in Eye Evolution: A Cnidarian PaxB Gene Uniting Pax2 and Pax6 Functions," Developmental Cell 5.5 (2003): 773-785.
Walter J. Gehring and Kazuho Ikeo, "Pax 6: mastering eye morphogenesis and eye evolution," Trends in Genetics 15:9 (1999), 371-377.
H
At 12:00 PM,
Joe G said…
Ya see David, you say you are writing a book about the rhetoric of anti-science.
It has fallen upon me to demonstrate you don't know anything about science.
This is just the beginning.
Hopefully next time you want to call someone out you will have second thoughts about doing so.
At 12:03 PM,
Hermagoras said…
"This is just the beginning."
I'm sorry. What do you mean by that?
At 12:55 PM,
Joe G said…
Umm again you demonstrate your ignorance-
PAX genes are HOX genes.
They are switches that control the development- ie does the eye develop or not.
Ya see David scientists have taken the PAX6 gene from a mouse and substituted into the genome of a fly.
The fly subsequently developed fly-eyes, not mouse eyes.
Did you read the OP?
What part of the following didn't you understand?:
That distinction goes to the control genes- that is the genes that control and direct cellular differentiation.
PAX genes are not responsible for cellular differentiation. They are switches- master switches to be sure- but only switches non-the-less.
At 1:00 PM,
Joe G said…
"This is just the beginning."
I'm sorry.
Yes you are.
What do you mean by that?
I'm just getting started. IOW I will take advantage of every opportunity to expose your ignorance.
I will also expose your lies- for example the lie in which you accuse my of threatening you.
Only a guilty intellectual coward (and general low-life) would think it is a threat that someone would say something to their face.
In reality I would just hand you my copy of "Fundamentals of Physiology & Anatomy" Martini fifth edition.
Then you could see what is required to get the human vision system. And you would also realize that your posting of that scientific paper does not refute my claim.
At 1:08 PM,
Hermagoras said…
Joe,
As I understand it, Pax6 contains a Hox gene but is not itself a Hox gene.
As for Pax6 as a control gene:
From Kozmik et al.:
"The well-characterized Pax6 has been considered a universal “master” control gene Gehring and Ikeo 1999 and Gehring 2002 for the morphologically distinct eye types generated in evolution (Land and Nilsson, 2002)."
H
At 1:19 PM,
Hermagoras said…
I should add that Kozmik et al. take issue with that characterization of Pax6 as a "universal" control gene, and in fact suggest a slightly more complicated trajectory:
"We propose that the ancestral gene PaxB was responsible for eye development in cnidarians, suggesting that it was the primordial gene for eye evolution, and that Pax6 arose from a common ancestor with PaxB in higher metazoans only after the separation of Cnidaria from Bilateria. This ancestral gene encoded a Pax2-like paired domain and octapeptide, and a prd-type homeodomain similar to modern PaxB in Tripedalia. In higher metazoa, the ancestral gene duplicated to generate Pax2 and Pax6. Pax2 lost most of its homeodomain but retained the octapeptide, while Pax6 conserved the prd-type homeodomain but lost the octapeptide."
Obviously these are contentious issues. But it seems to me we know a fair amount about the evolution of the visual system, and that what's happening now is that there are various competing narratives for which genes are exactly responsible for development of vision in which species etc. Do we know everything? No. Do we know a lot about the genetics of visual system evolution? You betcha.
At 1:26 PM,
Joe G said…
It is a master control gene. It controls whether or not the eye will develop, and develop correctly, in the organism.
It does not determine the type of eye.
PAX genes may regulate cellular differentiation during embryonic development, but they do not determine what cells become.
If it did than the fly would have developed mouse-eyes.
And again the vision system is much more than eyes.
At 1:28 PM,
Joe G said…
And you want to know something else- there isn't any scientific data that would demonstrate that the PAX genes, or any regulatory genes, arose (or can arise) via culled genetic accidents- ie the proposed mechanism of the anti-ID scenario.
At 1:44 PM,
Joe G said…
Pax6 induces ectopic eyes in a vertebrate:
"These data show that in vertebrates, as in the invertebrate Drosophila melanogaster, Pax6 is both necessary and sufficient to trigger the cascade of events required for eye formation."
Note the last part- after the second comma.
I would also love to see how Kozmik, et al.,
objectively tested their premise.
It could also be that PAX genes are part of the common design. We don't see different car companies redeign everything from scratch.
At 1:48 PM,
Hermagoras said…
Joe,
I'm of the view that no list of genes will satisfy you. More than that, I think you have posed the question in an unanswerable way. (I'm not sure if this is deliberate or not.) The truth is that there is no set of genes "responsible for" the visual system in the way you phrase it, because genes operate in the context of a variety of developmental systems. I'll quote Richard Lewontin on this:
"Geneticists speak casually of the 'gene for white eyes,' but, of course, there is no such gene. There is a variety of genes whose reading by the cell is proximally involved in the production of eye pigment and its deposition in the eye cells. One of these, the so-called white locus, can so be altered from its usual form by mutations that no eye pigment can be deposited. This gene is neither the gene 'for' white eyes nor the gene 'for' red eyes, and geneticists know that very well, yet the constant repetition of the language of genes 'for' white eyes or 'for' vestigal sings has a powerful effect on the conceptualization of the developmental process."
From that (developmental, systems) perspective, the question "Does anyone even know what gene or genes is responsible for the vision system?" can never be answered.
H
At 2:28 PM,
Hermagoras said…
You quoted the abstract. In the paper itself, Chow et al. point out the evolutionary implications of their work:
"Combined, these data show that in the context of the Xenopus embryo, Pax6 is necessary and sufficient for eye formation. These observations extend previous work performed in invertebrates (Halder et al., 1995; Czerny et al., 1999) to show that Pax6 can direct eye formation in a vertebrate. This argues strongly for the evolutionary conservation of the molecular mechanism involved in the genesis of the visual system in eyes as different as the compound eye of the insect and the camera eye of vertebrates and suggests a monophyletic origin for this important sensory organ."
Of course, as they say later,
"It may be something of an oversimplification to conclude from the presented data that Pax6 functions in isolation to direct normal eye development. The observation that ectopic eyes arise only in the head region argues that other factors are required and perhaps that only certain embryonic tissues are competent for eye formation. In Drosophila, misexpression of other genes such as sine oculis and eyes absent (Pignoni et al., 1997) or dachshund (Chen et al., 1997) can also lead to ectopic eye formation. It has been proposed that these genes, along with ey/Pax6, form part of a self-regulating network of genes whose combinatorial activity specifies eye formation."
Joe, you said,
"It could also be that PAX genes are part of the common design. We don't see different car companies redeign everything from scratch."
This is a very flexible comment. Any evolutionary conclusion can be contested the same way. Why argue about the science at all if you can just use "common design" as an escape catch?
At 3:32 PM,
Joe G said…
Umm when someone says:
"This argues strongly for the evolutionary conservation of the molecular mechanism involved in the genesis of the visual system in eyes as different as the compound eye of the insect and the camera eye of vertebrates and suggests a monophyletic origin for this important sensory organ."
They do so only via an a priori exclusion of any common design implication.
In order for anyone to say anything about evolutionary implications they must be able to account for the physiological and anatomical differences observed between the organisms that have this alleged conserved gene or set of genes.
Why argue about the science at all if you can just use "common design" as an escape catch?
Because genetic and morphological similarities can be explained by convergence or common design. IOW they are not the hallmark of descent with modification.
Why call it science when one cannot account for the physiological and anatomical differences?
At 3:39 PM,
Joe G said…
BTW I have already admitted that my wording may not have been correct.
THAT is why someone should ask for clarification before sticking their nose in something.
Also in order for there to be a plausible Darwinian explanation for the evolution of the vision system, there has to be a plausible Darwinian explanation for the evolution of single-celled organisms to something other than single-celled organisms.
IOW you guys can't even get out of the starting box.
The bottom-line is not everyone is as gullible as you are when it comes to biology.
Chapter VI “Why is a Fly not a horse?” (same as the book’s title)
"The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”- geneticist Giuseppe Sermonti.
Enough for now- back to the Pats and Sox...
At 6:35 PM,
Hermagoras said…
Joe, you write:
Umm when someone says:
"This argues strongly for the evolutionary conservation of the molecular mechanism involved in the genesis of the visual system in eyes as different as the compound eye of the insect and the camera eye of vertebrates and suggests a monophyletic origin for this important sensory organ."
They do so only via an a priori exclusion of any common design implication.
Design has nothing to do with the sentence. The point at issue in the sentence is whether the eye emerged only once, or several different times independently. They're arguing for the former.
H
At 8:26 PM,
Joe G said…
Design has nothing to do with the sentence.
No shit Sherlock. That's because, as I stated, they excluded common design, or any design, a priori.
The point at issue in the sentence is whether the eye emerged only once, or several different times independently. They're arguing for the former.
They are the minority. Good for them for "bucking the system".
I would still love to see the science behind the vision system emerging via culled genetic accidents.
BTW how about this question:
"Does anyone have any scientific data that the vision system could evolve via Dawrinian mechanisms (ie culled genetic accidents)?"
How would one test such a premise?
How could the premise be falsified?
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