Real Science Friday with a University of Cal Prof. of Ophthalmology

Jefferson

Administrator
Staff member
Administrator
Super Moderator
RSF with a University of Cal Prof. of Ophthalmology

This is the show from Friday, October 19th, 2012.

SUMMARY:

evolutions-witness.jpg


* RSF Interviews a University of California Professor of Ophthalmology
: Real Science Friday co-host Bob Enyart interviews UC San Francisco's clinical professor of opthamolgy Dr. Gary Aguilar. Before the interview, Gary recommended that Bob read a 2012 book by Dr. Schwab, a colleage of Aguilar's at UC Irvine, about which Russell Fernald says that Evolution's Witness is "likely to be consulted by everyone interested in evolution and eyes."

* Ivan Schwab's Evolution's Witness -- How Eyes Evolved: Within minutes of the mailman delivering this book, on March 31, 2012, Bob wrote on the title page, with a number of friends around him signing as witnesses: "Prediction: Very little of this book will be about how eyes evolve." Dr. Aguilar described this textbook as a "tour de force" showing clearly how eyes evolved. During today's interview, Bob asserts that his prediction was valid, and that 99% of this book has nothing to do with how eyes evolve. It's a great anatomy book though!

* The Opsin Missing Chapter: Opsin is the protein in photoreceptor cells that can detect a single photon and then signal that a photon has struck it. One might expect from a book on the eye's evolution, that after a book's introduction, the author might include a chapter on an explanation, conceptually, of how opsin might evolve. In vertebrates and invertebrates, opsin requires a chain of 150 to 250 amino acids, which then must be folded correctly into a very specialized nano-machine which can pass along an output signal whenever the protein gets hit with a single photon. But, as creationists would expect, no such chapter exists in the book. And actually, all the difficult problems that one would have to address if he were actually writing a book on "How eyes evolved," do not appear in the book.

* The PZ Myers Trochlea Challenge Missing Chapter: Six months before today's debate, I sent to Gary Aguilar our PZ Myers Trochlea Challenge, which evolutionary biologist PZ Myers admitted he could not answer. Gary offered no answer then, and if he ever does provide a reply, we'll be sure to present it here!

vision-challenge-data-stream.jpg


* Carbon 14 in Diamonds
: Early in the program Gary Aguilar could not understand how short-lived Carbon 14 might even theoretically be able to be used to falsify a claim that a particular specimen might be a million years old. Then at about 36 minutes in challenged Bob: I want you to find me a credible scientist who says that because of Carbon 14 in diamonds, that they have to be less than 7,000 years old. Because of the work of physicist Russell Humphreys, Bob was able to answer, "How about a scientist at Sandia National Labs, who has published on this?"


* Gary's "Good Christians": Dr. Aguilar recognizes that there are many Christians who believe like he does on many topics, including legalizing cocaine, belief in Darwinism, and holding an anti-Israel foreign policy. So, when he says, "good Christian," as he does often, one might think that he was referring to these Christians whom he agrees with. However, Gary never does that. He only uses the phrase "good Christian" when he refers to someone called a Christian who murdered, plundered, raped, etc. Then at about 50 minutes in, Gary, upset at Bob for opposing the decriminalization of heroin, crack, etc., said of Bob and of people like him, "You need to be set aside." About 50:30 into the show, Bob asks Gary if it is possible that his anger toward Christians causes him to be biased to automatically agree with Darwinists about evolution. He emphatically denied this: "I give no thought whatsoever to evolution or Darwinism." So, if Gary doesn't think about evolution, yet believes in it unequivocally, even to defending it's strongly refuted arguments (like the backwardly-wired eye), there must be something that is biasing him in that direction. It just seems that his passionate anger toward Christians might be the source of his bias.

For today's show Real Science Friday recommends
Dr. Carl Werner's DVDs, Living Fossils
and
its prequel Evolution, the Grand Experiment!


* Bob Too Slowly Replied to Gary's Moon Crater Question: Gary Aguilar was correct that Bob took too long to get around to answering his claim that all the craters on the moon are themselves proof of the passage of millions of years. Bob answered that because the near side of the moon has far more maria, or ""seas," which are the result of massive impactors, than does the far side, that this should help people realize that there is something wrong with the old-earth explanation of how those craters got there. Further, Bob never got around to explaining how NASA has learned, from inspection of a moon of Jupiter, that second-hand craters, that is, craters formed by debris thrown up by the impact of other craters, accounts for 95% of small craters and a significant percent of medium-sized craters. So, if the leading Big Bang cosmologists were commited to the data, or even to their theories, they would agree that therefore, the crater evidence on the moon suggests that it is significantly younger than they had previously claimed. For more, see our favorite astronomy DVD: What You Aren't Being Told About Astronomy! However, the ultimate commitment of the prevailing Darwinist and old-earth science communities is NOT the Big Bang, or descent with modification, etc., but atheistic materialism.


Today’s Resource: Get the fabulous Carl Werner DVD Living Fossils and his great prequel, Evolution: The Grand Experiment! And have you browsed through our Science Department in the KGOV Store? Check out especially Walt Brown’s In the Beginning! Also, you can consider our BEL Science Pack; Bob Enyart’s Age of the Earth Debate; Bob's debate about Junk DNA with famous evolutionist Dr. Eugenie Scott; and to give as a Christmas or birthday gift, the superb kids' radio programming, Jonathan Park: The Adventure Begins!
 
Last edited by a moderator:

Stripe

Teenage Adaptive Ninja Turtle
LIFETIME MEMBER
Hall of Fame
:darwinsm:

Please don't interrupt me! Don't interrupt me!
 

Jefferson

Administrator
Staff member
Administrator
Super Moderator
Dr. Aguilar gave a temper tantrum through that entire debate.
 

The Barbarian

BANNED
Banned

The Barbarian

BANNED
Banned
So, if the leading Big Bang cosmologists were commited to the data, or even to their theories, they would agree that therefore, the crater evidence on the moon suggests that it is significantly younger than they had previously claimed.

The maria are large lava flows that formed over areas of the moon. And they buried many craters as they went. We know this, because the buried craters sometimes are high enough to form "ghost craters" in the maria.
 

Frayed Knot

New member
Bob frequently says that C14 found inside a diamond can't be the result of contamination because diamonds are so hard.

I'll be generous here and assume Bob is simply mistaken on this. The contamination of added C14 to a sample is inevitable and a result of the processing that's done to a sample to get it ready for the mass spectrometer. No C14 atoms were found actually inside the diamond - we can't detect them there.

Some contamination of a sample is inevitable, and the smaller that a lab can guarantee that its contamination is, the older a date that they can reliably measure with C14. The best we can currently do is 50,000 or 60,000 years, and this limit is because even the best techniques result in a small amount of contamination.
 

The Barbarian

BANNED
Banned
Turns out, nitrogen is a very common inclusion in diamonds.
The most common impurity in diamond is nitrogen, which can comprise up to 1% of a diamond by mass.
http://prola.aps.org/abstract/PR/v115/i4/p857_1
http://en.wikipedia.org/wiki/Crystallographic_defects_in_diamond
http://archives.datapages.com/data/specpubs/mineral1/data/a176

C-14 is made when an atom of nitrogen is struck by ionizing radiation. So is there a source of such radiation in diamond-bearing deposits?

There is:
/a176/0001/0000/0036.htm

So it's not surprising if some of the nitrogen is, over time, converted to C-14.
 

Frayed Knot

New member
Thanks, Barbarian - I learned something.

I've looked around to try to find some discussion of intrinsic nitrogen converted to C14 by cosmic rays, and haven't found anything. There was the work of R.E. Taylor who used natural diamonds to calibrate the instrumentation uncertainty, which I think would assume that the diamonds had no C14 in them at all (so any detection of C14 would be due to the measurement process/preparation).

C14 in the atmosphere is caused by cosmic rays, but not from the cosmic ray interacting directly with a nitrogen atom. There's an intermediate step, where the cosmic ray triggers the release of a neutron, and this neutron is captured by a nitrogen atom, converting it into C14 (and ejecting a proton). I'm not aware of how this process would happen within a diamond. But the C14 then will decay back to nitrogen after a few thousand years or so. With diamonds, which are maybe one billion years old, if a nitrogen atom did get converted to C14, it likely would have already decayed back, because 5700 years is a blink in time compared to the age of the diamonds.

Then again, if nitrogen is 1% of natural diamonds, I could see that even if an extremely small proportion were currently converted to C14, this would be measurable because our detection equipment is so sensitive (they can detect one atom out of trillions).

I'm not sure where this leads, but the concentration of C14 in a diamond has been measured to be extremely low. Taylor was assuming it was zero for his purposes, but we're sure that it's so low that it's at or beyond the ability of our instrumentation to detect.
 

The Barbarian

BANNED
Banned
Thorium and uranium, among other radioactive isotopes, are found in kimberlite and other diamond-bearing rock. The release of radiation from these isotopes produce a cascade of different radiation effects. Some of these can efficiently covert nitrogen to C-14.

Of course, contamination at that very low level is possible, but there is no reason to be surprised that diamonds might contain C-14.
 

radd76

New member
The Not-so Mysterious (yet "Amazing") Opsins

The Not-so Mysterious (yet "Amazing") Opsins

The evolution of opsins isn't much of a mystery.
"Opsin requires a chain of 150 to 250 amino acids, which then must be folded correctly into a very specialized nano-machine which can pass along an output signal whenever the protein gets hit with a single photon."

That is getting to your opsin and it's not a mystery? That's communication on the nano level.

Notice that molecular biology shows that type I and type II opsins almost certainly evolved independently.

You just doubled your complexity to account for, congratulations! ...."Almost certainly"?....

(in the article you gave it states: "Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.")

If type I had evolved into type II then this would be touted as a iron clad evidence for evolution. Agh! But Evolution gets it both ways whether it comes together or stays totally separate... and we are talking about SIGHT here!

(Instead the article says things like this: Title: Opsins an amazing evolutionary convergence; Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!")

I don't know about you but if I had found something I was expecting I would not be "amazed" by it... lol. Just saying. I wish you guys could predict something based on evolution for a change instead of "reacting" to data that doesn't fit your expectations and making wild assumptions.

And yes, they started with simpler functions, before evolving a role in vision.

They did?

From your article: Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis.

Not simple. These are valuable functions in and of themselves.

:DK: I need to go listen to this thing!
 

The Barbarian

BANNED
Banned
Barbarian observes:
The evolution of opsins isn't much of a mystery.
"Opsin requires a chain of 150 to 250 amino acids, which then must be folded correctly into a very specialized nano-machine which can pass along an output signal whenever the protein gets hit with a single photon."

That is getting to your opsin and it's not a mystery? That's communication on the nano level.

Yep. And all natural. It might look astonishing to those who are unaware that a whole sequence of simpler opsins already existed before vertebrates.

The microbial opsin family of optogenetic tools.
Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J, Magnuson J, Hegemann P, Deisseroth K.
Cell. 2011 Dec 23;147(7):1446-57.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
The capture and utilization of light is an exquisitely evolved process. The single-component microbial opsins, although more limited than multicomponent cascades in processing, display unparalleled compactness and speed. Recent advances in understanding microbial opsins have been driven by molecular engineering for optogenetics and by comparative genomics. Here we provide a Primer on these light-activated ion channels and pumps, describe a group of opsins bridging prior categories, and explore the convergence of molecular engineering and genomic discovery for the utilization and understanding of these remarkable molecular machines.


Barbarian observes:
Notice that molecular biology shows that type I and type II opsins almost certainly evolved independently.

You just doubled your complexity to account for, congratulations! ...."Almost certainly"?....

Surprise.

(in the article you gave it states: "Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.")

If type I had evolved into type II then this would be touted as a iron clad evidence for evolution.

If that's what the evidence showed. But of course, things evolve in different ways. The evidence shows two different opsins evolved independently. Which is a very common thing in evolution.

But Evolution gets it both ways whether it comes together or stays totally separate...

Evidence, remember.

and we are talking about SIGHT here!

Not at first. They evolved first as other things. The visual opsins can be shown to have evolved from four gene duplication events. In bacteria, they evolved to a primitive form of photosynthesis.

There are a lot of different forms, of which a few are used in vision.

(Instead the article says things like this: Title: Opsins an amazing evolutionary convergence; Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!")

Yep. Go check out the evidence. Amazing.

I don't know about you but if I had found something I was expecting I would not be "amazed" by it... lol. Just saying. I wish you guys could predict something based on evolution

Let's take a look at some of those, then...

1. There must have been at one time, dinosaurs with feathers (Huxley) Confirmed.

2. There must have been at one time, whales with functional legs. Confirmed.

3. Insects should quickly evolve resistance to pesticides Confirmed

4. Genes should confirm the common descent of living things as in the nested hierarchy of taxa. Confirmed.

Stuff like that.

And yes, they started with simpler functions, before evolving a role in vision.

They did?

Yep. Bacteria use them for a primitive kind of photosynthesis.

From your article: Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis.

Not simple. These are valuable functions in and of themselves.

Of course. Evolution always modifies something already in use.
 

Bob Enyart

Deceased
Staff member
Administrator
Barbarian observes:

Bacteria use them for a primitive kind of photosynthesis.
Barbarian, the excerpt you started your own post with exposes the illusion that you are trying to create. You call this "primitive," but you're own reference states:

"microbial opsins... display unparalleled compactness and speed..."

Unparalleled. Nanotechnology. Physical reaction to discrete photons. You guys call extinct trilobites primitive, only because they're buried deep in the strata, to provide an illusion of evolution. But their eyes are known to be wildly, wildly, wildly, complex, especially when you include what we know today about the molecular technology that builds and maintains them.

Barbarian observes:

The evolution of opsins isn't much of a mystery.
"Opsin requires a chain of 150 to 250 amino acids, which then must be folded correctly into a very specialized nano-machine which can pass along an output signal whenever the protein gets hit with a single photon."​
Yep. And all natural.

Barbarian, do some rough math with me here. And correct me wherever I'm confused. Consider a ballpark estimate of the number of particles in the universe, what, 10 to the 80th? And allow them a million interactions with other particles per second. Let that experiment run for the duration of the universe. That's what, about 10 to the 24th interactions per particle, giving a total of about 10 to the 104 possible physical interactions, and let's throw in a billion other universes for a margin of error, all waiting, with no goal in mind, to come up with a functional sequence of amino acids that will be properly folded into a nano-machine that reacts to a striking photon. And how close does all that churning of matter get us to merely strike upon a functional order of acids to form an opsin? Not within a billion, trillion, universes. And then, evolution would have to to record the order of those amino acids, transliterated to three times its length, onto a DNA molecule, and to make sure that portion of the DNA is transcribed, and then find a way to fold that ordered strand, out of quadrillions of useless ways, into a functional form. And even then, that would accomplish nothing for sight unless that opsin was part of a sophisticated chain of necessary functional components. And then, if somehow the opsin's output found its way to the brain, rather than to, say, the hair, the brain would have to find a way to use symbolic logic to decode the meaning within the electrochemical data stream that happened upon it.

The "story" that evolutionists tell is awfully similar to the "story" that George Lucas tells in Star Wars. It's full of imaginary details that wrap around an actual physical framework to provide the illusion of reality.

-Bob Enyart

vision-challenge-data-stream.jpg
 

Bob Enyart

Deceased
Staff member
Administrator
Thorium and uranium, among other radioactive isotopes, are found in kimberlite and other diamond-bearing rock. The release of radiation from these isotopes produce a cascade of different radiation effects. Some of these can efficiently covert nitrogen to C-14.
Efficiently? Barbarian, have you seen the problems with your claim that we've presented at KGOV.com/14c ? (I've pasted the text there, here; but click on that link for references...)

* Problems with the Neutron Capture Explanation
First: Unexpected C14 is found in specimens worldwide, yet it takes a lot of nearby radioactivity to produce appreciable amounts of 14C by neutron capture. However, terrestrial radioactivity is concentrated, with the vast majority of it occurring in the continental crust. (On RSF Lawrence Krauss confirmed this well-documented observation.) Ninety percent of Earth's radioactivity is in 1/3rd of 1% of it's mass.
Second: Radioactivity is relatively scare even in the continental crust, at least as documented by this U.S.G.S. report for enormous swaths of land.
Third: Presented at the 2012 AGU Singapore conference, there was less than 20 parts per million of uranium and thorium in the dinosaur bones that contained large quantities of modern carbon, so much that it registered mid-range in the AMS (accelerator mass spectrometry) capabilities. (Uranium mines where the uranium content is 18% yield carbon specimens which have only 1% 14C, indicating that virtually none of the 14C in typical dinosaur bones is a result of neutron capture.)
Fourth: In a meeting with RSF, a geologist with a degree from Colorado's School of Mines who has a background in nuclear physics (who also spent years bombarding various elements with neutrons to make isotopes for industry) told RSF that Carbon does not easily absorb neutrons because it is the heavier elements beginning with Sodium that readily capture neutrons. Further, while it is relatively unlikely that a Carbon atom will capture a free neutron, industrial processes use Carbon to slow down neutrons, whereas they use heavier elements, typically starting with Silicon, which is almost double the atomic weight of Carbon, for neutron capture.
Fifth: Dr. Paul Giem writes that, "since nitrogen-14 captures neutrons 110,000 times more easily than does carbon-13," samples with even tiny amounts of nitrogen would dramatically increase carbon dates, such that, "If neutron capture is a significant source of carbon-14 in a given sample, radiocarbon dates should vary wildly with the nitrogen content of the sample." Giem adds, "I know of no such data."
Sixth: Recognizing that crustal radioactivity is generally relatively scare (as documented in this U.S.G.S report for coal, basalt, shales, granite, fly ash, etc.), Dr. Jonathan Sarfati builds upon Dr. Giem's research arguing that neutron capture could account for less than one 10,000th of the C-14 in diamonds (see these peer-reviewed calculations). Therefore, there would have to be thousands of times more uranium, thorium, etc. throughout the earth's crust everywhere that these globally dispersed materials are found.​

-Bob
 

Lon

Well-known member
:darwinsm:

Please don't interrupt me! Don't interrupt me!
Dr. Aguilar gave a temper tantrum through that entire debate.

"If you like, you can interrupt me, so we can have a conversation." -BE

He was already interrupting Bob way before that :chuckle:

He went overboard after that interrupting.

Bob - "Is it my turn?" :chuckle:
 

Frayed Knot

New member
Third: Presented at the 2012 AGU Singapore conference, there was less than 20 parts per million of uranium and thorium in the dinosaur bones that contained large quantities of modern carbon, so much that it registered mid-range in the AMS (accelerator mass spectrometry) capabilities. (Uranium mines where the uranium content is 18% yield carbon specimens which have only 1% 14C, indicating that virtually none of the 14C in typical dinosaur bones is a result of neutron capture.)

Are you sure it indicates that? If a sample has one percent of its carbon as C14, that's way way way higher than what we find in unaffected samples, so it's not obvious to me that 20 ppm of U and Th could not cause detectable levels of C14.


Fourth: In a meeting with RSF, a geologist with a degree from Colorado's School of Mines who has a background in nuclear physics (who also spent years bombarding various elements with neutrons to make isotopes for industry) told RSF that Carbon does not easily absorb neutrons...

My understanding is that you don't get C14 by C12 absorbing neutrons. It would have to absorb two, which would be really unlikely. C14 in the atmosphere is produced by a nitrogen atom absorbing a neutron and then ejecting a proton. There may be other paths to C14 that I don't know about, but I don't think that you can get there from C12.

What Barbarian and I were discussing earlier is that diamonds are about 1% nitrogen, so that's a lot of nitrogen atoms that could absorb neutrons. The levels of C14 that our mass spectrometers find in diamond are extremely extremely low, and those low levels could be explained by nitrogen atoms in the diamond crystal or by contamination in the preparation and measurement. My gut feel is that it's dominated by contamination, but I can't find data to support that one way or the other.
 

The Barbarian

BANNED
Banned
Barbarian observes:
Bacteria use them for a primitive kind of photosynthesis.

Barbarian, the excerpt you started your own post with exposes the illusion that you are trying to create. You call this "primitive," but you're own reference states:

"microbial opsins... display unparalleled compactness and speed..."

However, they are not very efficient at converting radiation to chemical energy, which is why most photosynthetic organisms use more evolved chemistry.

Unparalleled. Nanotechnology.

"Technology" is, of course the wrong idea for nature. God is not limited, and He has no need of figuring things out. Unless you're an IDer and think He might just be a "space alien."

Physical reaction to discrete photons.

Your skin can do that. No surprise there.

You guys call extinct trilobites primitive

There are primitive trilobites in the fossil record, but the late ones were rather highly evolved. And they diversified in to a great number of different lifestyles and habitats, one would hardly have guessed from their rather simple origins.

only because they're buried deep in the strata, to provide an illusion of evolution.

You've been misled about that. Scientists consider many ancient creatures to have been admirably adapted to their environments.

But their eyes are known to be wildly, wildly, wildly, complex

Some later ones. First ones we know about, didn't have eyes. Even most of the ones with eyes have the relatively simple holochroal form. But at least one adapted a lens that is essentially Huygen's design for minimal aberration. Not bad. But remember, they were evolving a lot longer than any mammalian line, so it's not surprising the later ones were so well-adapted.

Barbarian observes:
The evolution of opsins isn't much of a mystery.
"Opsin requires a chain of 150 to 250 amino acids, which then must be folded correctly into a very specialized nano-machine which can pass along an output signal whenever the protein gets hit with a single photon."

Yep. And all natural.

Barbarian, do some rough math with me here. And correct me wherever I'm confused. Consider a ballpark estimate of the number of particles in the universe, what, 10 to the 80th? And allow them a million interactions with other particles per second. Let that experiment run for the duration of the universe. That's what, about 10 to the 24th interactions per particle, giving a total of about 10 to the 104 possible physical interactions, and let's throw in a billion other universes for a margin of error, all waiting, with no goal in mind, to come up with a functional sequence of amino acids that will be properly folded into a nano-machine that reacts to a striking photon. And how close does all that churning of matter get us to merely strike upon a functional order of acids to form an opsin?

Indeed, if it was all at once by pure chance, it could never happen. But as you see from the opsin data, it happens gradually, and by natural selection. So the idea crashes on a false assumption.

The "story" that evolutionists tell is awfully similar to the "story" that George Lucas tells in Star Wars.

In this case, at least, you know better now.
 

Stripe

Teenage Adaptive Ninja Turtle
LIFETIME MEMBER
Hall of Fame
What Barbarian and I were discussing earlier is that diamonds are about 1% nitrogen

Fifth: Dr. Paul Giem writes that, "since nitrogen-14 captures neutrons 110,000 times more easily than does carbon-13," samples with even tiny amounts of nitrogen would dramatically increase carbon dates, such that, "If neutron capture is a significant source of carbon-14 in a given sample, radiocarbon dates should vary wildly with the nitrogen content of the sample." Giem adds, "I know of no such data."

My gut feel is that it's dominated by contamination, but I can't find data to support that one way or the other.
If contamination is so easily introduced and so difficult to rule out, why should we accept the certainty with which radiocarbon dates are presented?
 

The Barbarian

BANNED
Banned
If contamination is so easily introduced and so difficult to rule out, why should we accept the certainty with which radiocarbon dates are presented?

Dates of hundreds of thousands of years are indeed not accurate with C-14. It has a half-life of less than 6000 years, and this means that at those ages, so little would remain that it would be easily thrown off by contamination. It's rarely used by paleontologists, because it has such a short range. Used by archaeologists a lot, though.
 
Top