1. Evolution or Design? Duons

Posted on February 2, 2018 by J-Mac

Have you ever tried writing palindromes? How about writing phrases that can be read the same way in either direction? Here are some examples:
A man, a plan, a canal: Panama
Live not on evil
Was it a car or a cat I saw
These sentences were no doubt designed…
Can you imagine writing a book that can be read forwards and backwards containing 2 different stories that made sense? Not an easy task…

Watch the video and pay special attention to the following examples:

Alternative splicing of RNA that produces multiple proteins from one gene
Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
Dual coding genes in which one sequence is read in multiple frames to produce completely different protein

The magnitude of the dual coding problem in DNA would be the equivalent of writing a novel that could be read in either forward over reverse directions making two different stories both of which made sense…

And don’t forget that according to Darwinists the dual coding in DNA simply evolved, right?

403 thoughts on “1. Evolution or Design? Duons”

Entropy on February 2, 2018 at 1:55 am said:

A whole thread so that you can ignore the answers again?
Adapa on February 2, 2018 at 1:59 am said:

Another Creationist with the “gee this is soooo complex, therefore JESUS!” argument.

Can’t you guys ever come with anything new? Something besides your personal incredulity?
Joe Felsenstein on February 2, 2018 at 2:10 am said:

“Was it a car or a cat”

These sentences were no doubt designed…

For that one, it was designed, but was not a palindrome.

Now if it had instead said “Was it a car or a cat I saw” …
DNA_Jock on February 2, 2018 at 2:43 am said:

I am always puzzled when creationists / IDists tout poly-constrained DNA sequences as evidence of design, rather than haphazard evolution. If they actually thought about it for ten seconds, they would realize that such polyconstraints are something that designers avoid like the plague, but otoh they are something that one would expect to occasionally arise through an evolutionary “whatever works now” approach. And “occasionally” is how often we see them.
But actually thinking about it is not really their strong suit, I guess…
phoodoo on February 2, 2018 at 2:53 am said:

DNA_Jock:
I am always puzzled when creationists / IDists tout poly-constrained DNA sequences as evidence of design, rather than haphazard evolution. If they actually thought about it for ten seconds, they would realize that such polyconstraints are something that designers avoid like the plague, but otoh they are something that one would expect to occasionally arise through an evolutionary “whatever works now” approach. And “occasionally” is how often we see them.
But actually thinking about it is not really their strong suit, I guess…

They do? Hm…

PolyConstraints: a design pattern for flexible collaboration in heterogeneous mobile environments

http://ieeexplore.ieee.org/document/713540/

Like the plague, huh?
J-Mac on February 2, 2018 at 3:04 am said:

There is an error in that last sentence in bold letters.

It should be “Was it a car or a cat I saw”.

Thanks for noticing Joe!
I asked Neil to fix it.
stcordova on February 2, 2018 at 3:20 am said:

Great find J-mac. I learned a lot from that video so thank you for bringing it to my attention.

Richard Deem is an Old Earth/ID/Creationist. When I nearly left the Christian faith 18 years ago, his testimony helped hold me together. God bless him.

I’m posting now at spin-off of TSZ, TheSkepticalForum as I want to focus on gathering and recording material on various ideas. The forum format is more amenable to this since I don’t have to worry about infringing on the front pages of Blogs like TSZ. Plus, conversations and thread can be maintained for years as repositories of data.

Also, the new semester started at the NIH and I’m taking a class on neuro science. The first day of class was nice, not one word about evolutionary biology. I’m frankly tired of hearing and debating evolutionary biology than actually learning the way God’s creatures are put together and are “fearfully and wonderfully made”, just as the Christian God said in the Psalms.

FWIW, here is our textbook:

From Molecules to Networks, Third Edition: An Introduction to Cellular and Molecular Neuroscience 3rd Edition
….
An understanding of the nervous system at virtually any level of analysis requires an understanding of its basic building block, the neuron. The third edition of From Molecules to Networks provides the solid foundation of the morphological, biochemical, and biophysical properties of nerve cells. In keeping with previous editions, the unique content focus on cellular and molecular neurobiology and related computational neuroscience is maintained and enhanced.

All chapters have been thoroughly revised for this third edition to reflect the significant advances of the past five years. The new edition expands on the network aspects of cellular neurobiology by adding new coverage of specific research methods (e.g., patch-clamp electrophysiology, including applications for ion channel function and transmitter release; ligand binding; structural methods such as x-ray crystallography).

Written and edited by leading experts in the field, the third edition completely and comprehensively updates all chapters of this unique textbook and insures that all references to primary research represent the latest results.

The first treatment of cellular and molecular neuroscience that includes an introduction to mathematical modeling and simulation approaches
80% updated and new content
New Chapter on “Biophysics of Voltage-Gated Ion Channels”
New Chapter on “Synaptic Plasticity”
Includes a chapter on the Neurobiology of Disease
Highly referenced, comprehensive and quantitative
Full color, professional graphics throughout

It’s refreshing to study God’s Intelligent Designs than argue about evolutionary biology. The nervous systems is one of those designs.
Adapa on February 2, 2018 at 3:58 am said:

J-Mac starts an OP regurgitating some Creationist nonsense he doesn’t understand.

Phoodoo desperately Googles “polyconstraints” and posts the first thing he finds using the term.

Sal Cordova drops by to talk about his favorite subject, Sal Cordova.

Just another pleasant day at TSZ.
phoodoo on February 2, 2018 at 4:57 am said:

Adapa,

You forgot to mention DNA Jock and the plague.
DNA_Jock on February 2, 2018 at 11:49 am said:

phoodoo: They do? Hm…

PolyConstraints: a design pattern for flexible collaboration in heterogeneous mobile environments

http://ieeexplore.ieee.org/document/713540/

Like the plague, huh?

Safe to say that you didn’t read the article then.
Thank you for making my point re not even thinking about it for ten seconds.
Corneel on February 2, 2018 at 11:55 am said:

Can you imagine writing a book that can be read forwards and backwards containing 2 different stories that made sense? Not an easy task…

Richard Deem seemed to have inadvertently left out an example of two overlapping coding genes on opposite strands. A nice concrete example would help focus this discussion. Would you be so good to provide an example of that J-Mac? It shouldn’t be hard to find, given that the human genome seems to be replete with them.
dazz on February 2, 2018 at 12:29 pm said:

Here’s another palindrome: God Dog. Evolution or design?
phoodoo on February 2, 2018 at 12:53 pm said:

DNA_Jock: Safe to say that you didn’t read the article then.
Thank you for making my point re not even thinking about it for ten seconds.

The collaborating agents also keep changing their roles depending on the work to be performed at that time. In such situations, a simple and flexible handling of the transition between heterogeneous environments and roles is required. This paper proposes PolyConstraints, a design pattern to handle the generic problem of transitions across multiple network environments and roles.

Where does it talk about designers avoiding using polyconstaints like the plague? I guess I did miss that part.
Rumraket on February 2, 2018 at 1:00 pm said:

Adapa:
J-Mac starts an OP regurgitating some Creationist nonsense he doesn’t understand.

Phoodoo desperately Googles “polyconstraints” and posts the first thing he finds using the term.

Sal Cordova drops by to talk about his favorite subject, Sal Cordova.

Just another pleasant day at TSZ.

This. ^^
keiths on February 2, 2018 at 1:08 pm said:

phoodoo,

That design pattern is for dealing with polyconstraints, not creating them.

I would revoke your Google license, if there were such a thing.
Rumraket on February 2, 2018 at 1:14 pm said:

“And don’t forget that according to Darwinists the dual coding in DNA simply evolved, right?”

Yes. Epistasis. Done.
Corneel on February 2, 2018 at 1:20 pm said:

Watch the video and pay special attention to the following examples:

Alternative splicing of RNA that produces multiple proteins from one gene
Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
Dual coding genes in which one sequence is read in multiple frames to produce completely different protein

I watched the video and payed special attention to the examples. It could be me, but neither the video nor the OP seems to mention why these are good design decisions. Wouldn’t it be better to have different proteins coded by different genes so their transcription doesn’t interfere? The only possible advantage I could think of are if there are severe genome size restrictions like viruses have (which indeed often have overlapping genes).

ETA: molecular functions => proteins.
Entropy on February 2, 2018 at 1:29 pm said:

Corneel: I watched the video and payed special attention to the examples. It could be me, but neither the video nor the OP seems to mention why these are good design decisions.

Yeah, it looks as if shit just happens. This clumsy designer.

Corneel: Wouldn’t it be better to have different molecular functions coded by different genes so their transcription doesn’t interfere?

Yeah! Finer control, all that stuff.

Corneel: The only possible advantage I could think of are if there are severe genome size restrictions like viruses have (which indeed often have overlapping genes).

Because this magical designer has no choice but to make tiny-tiny thingies to infect all kinds of cells. Of course.
Rumraket on February 2, 2018 at 2:16 pm said:

Corneel: The only possible advantage I could think of are if there are severe genome size restrictions like viruses have (which indeed often have overlapping genes).

And yet viruses evolve like crazy. But shouldn’t overlapping genes and transcription make that impossible? Yet it doesn’t.

The Effect of Gene Overlapping on the Rate of RNA Virus Evolution.

In general they exhibit a reduced rate compared to non-overlapping genes, but not zero rate. And RNA viruses still evolve much faster than multicellular eukaryotes do in general.
phoodoo on February 2, 2018 at 2:32 pm said:

keiths:
phoodoo,

That design pattern is for dealing with polyconstraints, not creating them.

I would revoke your Google license, if there were such a thing.

https://books.google.com.hk/books?id=AuH7CAAAQBAJ&pg=PA42&lpg=PA42&dq=polyconstraints&source=bl&ots=4FlUo9tI3z&sig=DqI9NCgT1d3OK1Rc5QUlPYDBTBM&hl=en&sa=X&ved=0ahUKEwjxh6upt4fZAhUMWbwKHStWBSQQ6AEIRjAH#v=onepage&q=polyconstraints&f=false

Page 44 keiths:

“Here polyconstraints can be useful, allowing one to thicken the grid and to avoid using triangles at the same time.”

Maybe they mean to avoid getting the plague?
Rumraket on February 2, 2018 at 2:37 pm said:

phoodoo: Page 44 keiths:

“Here polyconstraints can be useful, allowing one to thicken the grid and to avoid using triangles at the same time.”

Maybe they mean to avoid getting the plague?

Wow, you found that single sentence. That’s great phoodoo. What does it mean though?
Corneel on February 2, 2018 at 3:03 pm said:

Rumraket: Wow, you found that single sentence.

Don’t you hate that, when you want to thicken the grid but you can’t because you have to avoid those %*&% triangles.
stcordova on February 2, 2018 at 4:27 pm said:

J-mac,

As an aside, since I won’t be able to participate in discussion of this excellent topic much, I’m working on re-training myself in quantum mechanics. You might be interested in how I connecting quantum mechanics (albeit incompletely) from Bohr to God and Intelligent Design:

http://theskepticalforum.org/index.php?topic=347.new#new

I’ll be adding to the QM thread(s) as time goes on, God willing…

God bless,
Sal
Rumraket on February 2, 2018 at 4:55 pm said:

For the low price of your critical faculties, you too can join Salvador Cordova to engage in absolute and credulous sycophancy. The opportunity of a lifetime. 🙂
stcordova on February 2, 2018 at 5:30 pm said:

Rumraket:
For the low price of your critical faculties, you too can join Salvador Cordova to engage in absolute and credulous sycophancy. The opportunity of a lifetime.

Physics is the real deal, evolutionary biology makes me vomit intellectually. It pretends with its “abstruse theorems” that it’s like physics, but it only pretends. The real deal is physics. That’s why I hope I can find the discipline to be here at TSZ less and less because:

In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to [the pseudo sciene of] phrenology than to physics.

Jerry Coyne

So, I’ve decided to revisit what I once studied, namely physics. I’m fed up with evolutionary biology. I find the discipline utterly unscientific, untestable, speculative and ugly and pseudo scientific. Quantum Mechanics is sublime and beautiful by comparison.

J-mac, here is the thread on Schrodinger’s equation if you’re at all interested. There is more science in Schrodinger’s equation than all the books on evolutionary biology combined:

http://theskepticalforum.org/index.php?topic=361.msg417#new
keiths on February 2, 2018 at 5:31 pm said:

Rumraket, to phoodoo:

Wow, you found that single sentence. That’s great phoodoo. What does it mean though?

Yes, do tell us, phoodoo.
keiths on February 2, 2018 at 5:33 pm said:

Sal:

I’m fed up with evolutionary biology. I find the discipline utterly unscientific, untestable, speculative and ugly and pseudo scientific.

…states someone who is utterly unqualified to render that judgment.
GlenDavidson on February 2, 2018 at 5:43 pm said:

stcordova: I’m fed up with evolutionary biology. I find the discipline utterly unscientific, untestable, speculative and ugly and pseudo scientific.

And even worse, you can’t refute it legitimately.

But oh, you can certainly ape the impotence of other IDists and demonize real science, while clinging to superstition.

Glen Davidson
J-Mac on February 2, 2018 at 5:43 pm said:

stcordova,

Hey Sal,

Who is the owner and the moderator of theskepticalforum.org?
You or Alan?
DNA_Jock on February 2, 2018 at 5:56 pm said:

stcordova: So, I’ve decided to revisit what I once studied, namely physics. I’m fed up with evolutionary biology. I find the discipline utterly unscientific, untestable, speculative and ugly and pseudo scientific. Quantum Mechanics is sublime and beautiful by comparison.

Says the chap who thinks that ∂ΔH/∂T is a second derivative!
ROFL
J-Mac on February 2, 2018 at 5:56 pm said:

stcordova,

Hi Sal,
QM is deep… and yet extremely fascinating…
I will have a look at the TSF over the weekend…
The connection between QM and ID/God is obvious, if you don’t have a materialistic veil over your eyes…
Unfortunately, there seems to be another level of reality below QM, which I call subquantum: dark energy and dark matter…
We know it’s there but we can’t detect it except for its effects… It’s kind of like God… 🙂
My advice for you would be: ask yourself why you want to learn QM. I got into it because of consciousness vs soul …
Why are you doing it?
J-Mac on February 2, 2018 at 6:21 pm said:

Quote from the video:

12:22
“..Almost universally, when we have a mutation that shifts the reading frame,
it is almost always bad since it totally destroys the current protein sequence …”

Which evolution obviously predicts…
The creative power of the mutational destruction…Sound familiar? Joe?
stcordova on February 2, 2018 at 6:22 pm said:

J-Mac:
stcordova,

Hey Sal,

Who is the owner and the moderator of theskepticalforum.org?
You or Alan?

Alan is the owner, Alan and Neil are the admins, everyone else are moderators.

The reason I chose that venue is that hostile critics occasionally give me valuable editorial corrections. I’m trying out some of my teaching material there.

As to why I’m exploring Quantum Mechanics, I delight in studying God’s creation and Intelligent Design, I’ve gotten my fill of evolutionary biology. Enough is enough.

The QM stuff in my threads is mostly straight out of Griffiths. The first few comments are the most accessible, the remaining parts get way into the weeks and is mostly my personal notebook in self-study of the math in physics.
Rumraket on February 2, 2018 at 6:32 pm said:

stcordova: Physics is the real deal, evolutionary biology makes me vomit intellectually.It pretends with its “abstruse theorems” that it’s like physics, but it only pretends.The real deal is physics. That’s why I hope I can find the discipline to be here at TSZ less and less because:

So, I’ve decided to revisit what I once studied, namely physics.I’m fed up with evolutionary biology.I find the discipline utterly unscientific, untestable, speculative and ugly and pseudo scientific.Quantum Mechanics is sublime and beautiful by comparison.

J-mac, here is the thread on Schrodinger’s equation if you’re at all interested.There is more science in Schrodinger’s equation than all the books on evolutionary biology combined:

http://theskepticalforum.org/index.php?topic=361.msg417#new
Entropy on February 2, 2018 at 6:50 pm said:

The most amazing thing is that J-Mac thinks that the overlapping portions of overlapping genes are as lengthy as novels. Maybe the novels J-Mac reads consists on a maximum of one sentence each.
keiths on February 2, 2018 at 7:05 pm said:

J-Mac,

What do you do for a living? I’m sure I’m not the only curious person out here.

colewd,

Same question. I know you were a semiconductor tester operator at one point. What do you do now (or what did you do before you retired)?
John Harshman on February 2, 2018 at 7:14 pm said:

stcordova: There is more science in Schrodinger’s equation than all the books on evolutionary biology combined

So much for respecting Joe Felsenstein’s work. Or mine. I assume you will retract all such prior statements.
colewd on February 2, 2018 at 7:23 pm said:

keiths,

Same question. I know you were a semiconductor tester operator at one point. What do you do now (or what did you do before you retired)?

Most of my career was in management in the semiconductor and semiconductor equipment industry. I was never a test equipment operator but had operators report to me in the past. My last job was VP of global operations for a division of Applied Materials.

I retired from corporate life in 2001 however I helped two distressed companies turn operations around as cfo/ceo as part of my investing activities. I am currently an investor and part owner in 3 ongoing businesses in food production, real estate and restaurants.
Neil Rickert on February 2, 2018 at 7:54 pm said:

stcordova: The reason I chose that venue is that hostile critics occasionally give me valuable editorial corrections.

But you might be talking to yourself.
keiths on February 2, 2018 at 9:32 pm said:

Thank you, Bill.

I’m finding it hard to reconcile your abysmal reasoning skills with your role as a corporate turnaround specialist. Have you experienced any traumatic head injuries since then?
Entropy on February 2, 2018 at 9:46 pm said:

Salvador’s opinions in science seem to be reduced to “if it’s too complicated to be explained in a single tiny equation, fitting the observations with high accuracy, it’s not science!”

Because, well, life is so damn simple, that its evolution should also fit into a single equation with but one variable, and we should get the whole history of life right there! What’s wrong with these biologists? Why do they study all those complex things? That’s not science. Science is when you have a simple phenomenon, you put that into an equation, and you’re done!

I’m vomiting too.
J-Mac on February 2, 2018 at 9:48 pm said:

stcordova: Alan is the owner, Alan and Neil are the admins, everyone else are moderators

So…nothing changes when it comes to censorship…
Why would I even consider posting there?
Plus, I don’t like the forum setup… but that’s just my preference…
J-Mac on February 2, 2018 at 9:53 pm said:

Adapa:

Who is forcing you to read TSZ?
If you like reading what you want to hear, subscribe to Fake News for Darwinoosaurs…
J-Mac on February 2, 2018 at 10:10 pm said:

dazz: dazz

dazz,

Your obsession with ass is obvious…You don’t have to make it public…
Have you ever thought of changing your name to dass or gass? (G being for grande ass)
It’d definitely suit your name with your preoccupation with asses better…
keiths on February 2, 2018 at 10:13 pm said:

J-Mac,

Did you see this?

What do you do for a living? I’m sure I’m not the only curious person out here.
J-Mac on February 2, 2018 at 11:21 pm said:

stcordova,

How about investigating QM with the relation to mutations?
Even some reasonable materialists agree that everything material is run by QM.. one subatomic level of course…
colewd on February 3, 2018 at 2:14 am said:

keiths,

I’m finding it hard to reconcile your abysmal reasoning skills with your role as a corporate turnaround specialist. Have you experienced any traumatic head injuries since then?

A turn around problem is never solved with group think. The atheist worldview you share is the ultimate group think perspective. I understanding the reasoning that contradicts your worldview appears abysmal. Michael Lewis just published a book about this.
Adapa on February 3, 2018 at 4:58 am said:

J-Mac: Who is forcing you to read TSZ?
If you like reading what you want to hear, subscribe to Fake Newsfor Darwinoosaurs…

I read Creationist comments like yours because I’m both fascinated and amused by the depths of scientific ignorance and stupidity they constantly reach in trying to defend their religious mythology.
OMagain on February 3, 2018 at 9:51 am said:

keiths: Did you see this?

Morton’s daemon is strong with the current batch. So I’m guessing, no.
OMagain on February 3, 2018 at 10:11 am said:

Regarding the OP, I’ve made extensive comments about this exact issue several times and specifically to J-Mac if I recall correctly. However he did not engage seriously with me then and given the evidence of intent in this thread so far

J-Mac: Your obsession with ass is obvious

I don’t think it’s worth the effort.

In case anyone is wondering, the ignore button is now the little ‘X’ next to the timestamp on the message.