Deplorable words?: DNA is NOT the blueprint for life?

_{April 23, 2020

Genetics, Genomics, Intelligent Design}

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Remember the guy who showed us a CD of his genome and said this is me? Naw, we didn’t think so at the time either, but read on:

The common view of heredity is that all information passed down from one generation to the next is stored in an organism’s DNA. But Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, disagrees.
In two new papers, Jose argues that DNA is just the ingredient list, not the set of instructions used to build and maintain a living organism. The instructions, he says, are much more complicated, and they’re stored in the molecules that regulate a cell’s DNA and other functioning systems.
Jose outlined a new theoretical framework for heredity, which was developed through 20 years of research on genetics and epigenetics, in peer-reviewed papers in the Journal of the Royal Society Interface and the journal BioEssays. Both papers were published on April 22, 2020. Jose’s argument suggests that scientists may be overlooking important avenues for studying and treating hereditary diseases, and current beliefs about evolution may be overly focused on the role of the genome, which contains all of an organism’s DNA.
Kimbra Cutlip, University of Maryland, “DNA may not be life’s instruction book—just a jumbled list of ingredients” at Phys.org

Papers:

Antony M. Jose, A framework for parsing heritable information, Journal of The Royal Society Interface (2020). DOI: 10.1098/rsif.2020.0154 (open access)

Antony M. Jose. Heritable Epigenetic Changes Alter Transgenerational Waveforms Maintained by Cycling Stores of Information, BioEssays (2020). DOI: 10.1002/bies.201900254 (paywall)

If this kind of stuff holds up and continues, our splintered lectern recycling sideline is going to be keeping us pretty busy. Cruel people say that’s what we’re really in this for. But you, loyal readers, know that that’s not true. Sure, we care about the environment. But the world of ideas… the world of ideas …

Hat tip: Philip Cunningham

Comments

Previously at post 9, JVL claimed that DNA being "triggered based on chemical considerations" was enough, in and of itself, to explain how an adult organism might achieve its basic form and or shape during embryological development.
"Different parts of the DNA ‘recipe’ are triggered based on chemical considerations in the developing embryo." - JVL
Here is a video that shows JVL's claim is patently false,
The (Electric) Face of a Frog - video https://www.youtube.com/watch?v=0VULjzX__OM
As the researcher stated, "I would never have predicted anything like it. It's a jaw dropper."
Timelapse Video Reveals Electric Face in Embryonic Tadpole - July 2011 Excerpt: "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo. We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It's a jaw dropper." http://www.sciencespacerobots.com/timelapse-video-reveals-electric-face-in-embryonic-tadpole-718111
In fact, altering the bio-electric field without altering the underlying molecules, affects the three-dimensional shape of the developing embryo.
podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes outside of DNA are discussed) – Oct. 2015 – 4:45 minute mark 5.Bio-electric code – altering the bio-electric field without altering the underlying molecules affects the three-dimensional shape of the developing embryo http://www.discovery.org/multimedia/audio/2015/10/id-inquiry-jonathan-wells-on-codes-in-biology/#more-31141
In the case of frog embryos, “artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm.
Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation – January 2013 Excerpt: A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. http://www.ncbi.nlm.nih.gov/pubmed/23802040
To date, no one knows how the 'bioelectric code' is supposedly encoded within the developing embryo's molecules, as is presupposed with Darwinian materialism, and although there is great interest in understanding exactly how such a 'jaw dropper' happens
The bioelectric code: An ancient computational medium for dynamic control of growth and form. – 2017 Excerpt: We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering. https://www.ncbi.nlm.nih.gov/pubmed/28855098
As the following article states, "such manipulations have produced conflicting outcomes experimentally, which poses a substantial barrier to understanding the fundamentals of bioelectrical reprogramming."
The Bioelectric Code: Reprogramming Cancer and Aging From the Interface of Mechanical and Chemical Microenvironments – March 2018 Excerpt: there is considerable interest in manipulating Vm both to treat cancer as well as to regenerate organs damaged or deteriorated during aging. However, such manipulations have produced conflicting outcomes experimentally, which poses a substantial barrier to understanding the fundamentals of bioelectrical reprogramming. https://www.frontiersin.org/articles/10.3389/fcell.2018.00021/full
To say that all of this is antagonistic towards the presuppositions of Darwinian materialism and favorable towards ID presuppositions would be an understatement. Verse:
John 1:4 In him was life, and that life was the light of all mankind.
bornagain77_{April 26, 2020
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ET: Chromosomes never change the end product. You get a deformed human or sterile mules. The same body plan as the original. I would call that a different end product but seeing how you are using the term clears up some of my questions to you. That's it, thanks.JVL_{April 25, 2020
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JVL:
How common are those?
Very
Hang on, does that mean some mutations do affect function?
If the design allows for it.
Why three?
More than 3. Because waiting for two mutations is close to impossible for populations like primates. Gene duplication is useless without a new binding site. And even then it has to end up on the proper part of the spool to be of any use. After all that all you are doing is getting more of an existing protein. One that is free to float around and get in the way.
With duplications you’re implying there should be no affect but I don’t think that is the case.
You don't get to tell me what I am implying. I was talking specifically about changes in the sequence of an existing protein. A gene duplication will bring on the same existing protein, if it gets regulated at all. Chromosomes never change the end product. You get a deformed human or sterile mules. The same body plan as the original.ET_{April 25, 2020
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ET: Synonymous changes can have either no effect or be detrimental. Then there are changes at the amino acid level, ie one hydrophobic amino acid for another. Or one hydrophilic amino acid for another. Okay. How common are those? Opsin genes appear to be tunable. It seems that specific differences allow for vision @ different wavelengths. Hang on, does that mean some mutations do affect function? Which ones do and which ones don't? And any mutational sequence that requires more than 3 specific mutations would be a good candidate for directed mutations. Okay. Why three? What about two? What about one? What about gene duplication? What about chromosomal duplication? With duplications you're implying there should be no affect but I don't think that is the case. Certainly not with chromosomes.JVL_{April 25, 2020
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JVL:
what kind of changes can occur which have no affect on the “final product”
Synonymous changes can have either no effect or be detrimental. Then there are changes at the amino acid level, ie one hydrophobic amino acid for another. Or one hydrophilic amino acid for another. Opsin genes appear to be tunable. It seems that specific differences allow for vision @ different wavelengths. And any mutational sequence that requires more than 3 specific mutations would be a good candidate for directed mutations.ET_{April 25, 2020
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ET: And some can’t take any hits without becoming useless or harmful- sickle-cell anemia is one such instance. So, again, I'm asking: what kind of changes can occur which have no affect on the "final product" and what changes are important? And, the obvious follow-on question would be: are any of these changes directed and how can you tell which ones are?JVL_{April 25, 2020
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As I said, take a biology course. Most proteins have more than one coding sequence that produces the same functional protein. Andreas Wagner goes over this in his book. He said that some proteins can handle over 80% change in sequence and still be the same functional protein. And some can't take any hits without becoming useless or harmful- sickle-cell anemia is one such instance.ET_{April 25, 2020
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Upright BiPed: JVL, as you can see, my comment wasn’t addressed to you. Yes, I see that now, my apologies.JVL_{April 25, 2020
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ET: Do you have any evidence that unguided processes can produce a protein? No. Do you have any evidence that unguided processes can produce coding DNA? No. Do you know what determines form? No. Well, I think there are answers to those questions but I'd really like to hear what you think first if that's okay! Mutations don’t have to occur in coding sequences. hence the word “potentially”. It would be better to discuss biology with people who know and understand the subject. I'm still trying to understand how mutations can affect coding sequences but have no affect on the final product. If things are produced in a different sequence then you get a different folding of a protein at the very least I should think. And what kind of changes can proteins take and not be altered? Do you have any examples?JVL_{April 25, 2020
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. JVL, as you can see, my comment wasn't addressed to you. You have already suggested that you don't know enough to carry on a conversation about the evidence for design in biology (and apparently dis-interested in learning anything), and I have agreed with you.Upright BiPed_{April 25, 2020
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Do you have any evidence that unguided processes can produce a protein? No. Do you have any evidence that unguided processes can produce coding DNA? No. Do you know what determines form? No. Mutations don't have to occur in coding sequences. hence the word "potentially". It would be better to discuss biology with people who know and understand the subject.ET_{April 25, 2020
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ET: Does it? Care to try to make a case? You said: DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. That's not qualified; DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. Then you said: Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101. So some changes do make a difference, yes? But you think most do not? There are few, if any changes that affect functionality of the organism? What about repeats of base pairs or even whole genes or chromosomes? With repeats nothing is changed there's just an extra copy. Does that have an effect on the organism? Upright BiPed: This is regularly demonstrated among materialists by their uniform inability to attack the observations and history, instead of their opponents. I'm attacking no one. I'm asking questions about the science. Do you agree with ET when he (?) says: Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. Is he just hedging his bets by saying potentially?JVL_{April 25, 2020
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#41 A living cell is a description-based organization. The quiescent description requires a multi-referent symbol system (I.e. discontinuous association); the onset of spatial orientation, a coordinated set of non-integrable constraints, and semantic closure in order to even begin to function -- to persist over time. It is all just as it was predicted to be, and fully documented in the literature. You are whistling past the graveyard. This is regularly demonstrated among materialists by their uniform inability to attack the observations and history, instead of their opponents.Upright BiPed_{April 25, 2020
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JVL:
Depends on the mutation then doesn’t it?
Does it? Care to try to make a case? Creating a broken protein doesn't help you, duh. But it is all your side has- a mechanism that can break things.ET_{April 25, 2020
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Jimmie T, strawman hunter. No one has said that DNA doesn't matter. Evos are such a clueless lot.ET_{April 25, 2020
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@JVL If the DNA doesn’t matter, then that destroys one of intelligent design’s biggest arguments. I mean, it was a dumb, clueless argument to begin with, but that just wrecks it further.Jim Thibodeau_{April 25, 2020
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ET: Take a biology course. Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101. Depends on the mutation then doesn't it? Andreas Wagner’s book goes over that- that proteins are robust in that they can accept changes to the sequence but not change the final protein product. But what is even stranger than that is there can be a synonymous change in the sequence that does have an effect on the protein. Again, that depends on the mutation doesn't it? Some mutations break things as you've pointed out many times. Which means there is a change in the final product. So, it's a little bit more complicated.JVL_{April 25, 2020
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JVL:
How can mutations affect the coding sequence but have no affect on the final product?
Take a biology course. Proteins do not have only one sequence that can produce it. Most proteins can take many changes and not be altered. Biology 101. Andreas Wagner's book goes over that- that proteins are robust in that they can accept changes to the sequence but not change the final protein product. But what is even stranger than that is there can be a synonymous change in the sequence that does have an effect on the protein.ET_{April 25, 2020
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ET: DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. How can mutations affect the coding sequence but have no affect on the final product? Does the coding sequence not matter then? At all? What's it for then? You did say "DNA controls and influences development" but then you said changes don't affect the final product.JVL_{April 25, 2020
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When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll.
You just described over 99% of all evolutionists. Nice own goal.ET_{April 25, 2020
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It's very telling that evos always try to make this personal when there unscientific ways are exposed. DNA controls and influences development. It also codes for proteins and other biologically relevant macromolecules. Mutations can potentially change the coding sequence and yet have absolutely zero effect on the final product. And guess what? Evos don't have anything to account for any of that.ET_{April 25, 2020
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JimThibodeau: When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll. I try and treat everyone with respect and give them the benefit of the doubt. Otherwise we're just taunting each other and not getting anywhere.JVL_{April 25, 2020
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Yes, Jimbo, and I explained why. But thanks for continuing to prove that you are willfully ignorant. You don't know anything about science, Jim. That is why you avoid all discussions pertaining to science.ET_{April 25, 2020
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@JVL Do you recall when ET admitted that he’s never bothered to show his revolutionary new infinity series math to any mathematician? Or put it forth to the mathematical community in any way? That was a tacit admission that he knows he full of caca. When you encounter someone who pretends to study science, but never bothers to put in the work, or participate in the community, you’re not talking to someone serious. You’re talking to a troll.Jim Thibodeau_{April 25, 2020
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ET: There isn’t anything in DNA that determines form. There isn’t anything in DNA that determines what type of organisms will develop. Well, what do you think the DNA does then? What's it for? How do mutations affect its function?JVL_{April 25, 2020
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Jawa: Everyone makes mistakes, that’s why they have proofreaders that detect errors before the text goes public. Yours is a cheap excuse that doesn’t work in this case. Try again. You are making a mountain out of a molehill. I've found typographical erros in printed books for as long as I can remember. Lots of websites allow the authors to publish their posts after only a cursory glance by their editor. AND, again, the mistake you pointed out was very peripheral to the main point of the post. Which was very, very clear. No, you didn’t get it yet. The real point (not only mine) is to highlight errors that have been made in the past because many scientists have been narrow minded, lacking humility to search for answers instead of jumping into conclusions before verifying them. It's not perfect but that is exactly why reputable scientific journals have a system of peer-review. Most research papers are not just tossed onto a page without several people taking a good look at them. And there is always someone out there who would love to take someone else down a peg or two. And all results can be tested again by anyone who is interested in double checking. If you think most of recent biological research is rubbish then you are welcome to check it out yourself. Or do work you think IS pertinent and on target. In some cases that narrow mindedness has caused delays in scientific research that could have been prevented otherwise. It’s a pathetic reality nobody can honestly deny. For example? Barking up the wrong tree is not a scientific attitude. Do you understand this now? Herd mentality consensus may not work in science. Do you want to understand it? Give it a try. As IBM used to remind many years ago: think. Just out of curiosity, what scientific work have you done and published? Does your opinion come from experience doing the work?JVL_{April 25, 2020
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There isn't any analogy between DNA and a recipe. And there isn't any need to put scare-quotes around the word code when referring to DNA coding for proteins. There isn't anything in DNA that determines form. There isn't anything in DNA that determines what type of organisms will develop. And that means neither Darwin nor anyone who accepts universal common descent has a mechanism capable of producing the diversity of lifeET_{April 25, 2020
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Did Dr Lee Cronin get the Evo2.0 $10M OOL prize yet? :)jawa_{April 25, 2020
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DNA may not be life's instruction book—just a jumbled list of ingredients by Kimbra Cutlip, University of Maryland
For example, the gene for eye color exists in every cell of the body, but the process that produces the protein for eye color only occurs during a specific stage of development and only in the cells that constitute the colored portion of the eyes. That information is not stored in the DNA.
Actually, it's much more interesting than that. Part of the information for the given example is stored in the DNA: the actual "gene" code to be translated to protein, the introns to be spliced out, the ncRNA transcripts that could intervene in some regulatory processes, the promoter region (TATA box, etc), the TF-binding sites (landing pads) near the promoter regions, the enhancers, the DNA bending proteins attached to the enhancers, etc. Other required information for the given example could be "stored" in the epigenetic markers, in the histone codes, in the extra-membrane receptor and the transduction signaling pathways (cascades) that must produce the right code to dovetail the TF-binding sites containing the patterning code, etc. The real deal is that all that stuff must match, which means that the whole choreography and its accompanying orchestration must have been designed to match. How else could one explain it? As Salieri told the catholic priest that visit him in the Oscar-winning movie "Amadeus", referring to WA Mozart's music, we're staring at an absolute beauty. :) That's why the heated discussions on multi-verse to cover the fine-tuning, Penrose's cyclical eons, dark matter/energy, inflation, and all that paraphernalia, could be kind of entertaining, but the real issue is how do we explain the undeniable evidences of complex functionally specified information that are increasingly revealed by fascinating discoveries made by seriously dedicated biology researchers these days and in the days to come? At the end of the OP-cited article:
generalization of memory and encoding via the entity-sensor-property framework sheds novel insights into evolution and biological complexity and suggests important revisions to existing paradigms in genetics, epigenetics and development
Can someone honestly offer an alternative?jawa_{April 25, 2020
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JVL @25, “Is your real point that the wrong impression has been given out in the past or shall we discuss what is correct? “ No, you didn’t get it yet. The real point (not only mine) is to highlight errors that have been made in the past because many scientists have been narrow minded, lacking humility to search for answers instead of jumping into conclusions before verifying them. In some cases that narrow mindedness has caused delays in scientific research that could have been prevented otherwise. It’s a pathetic reality nobody can honestly deny. Barking up the wrong tree is not a scientific attitude. Do you understand this now? Herd mentality consensus may not work in science. Do you want to understand it? Give it a try. As IBM used to remind many years ago: think. :)jawa_{April 25, 2020
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