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I’ve long suspected the 3.1 to 3.5 gigabases of human DNA (which equates to roughly 750 to 875 megabytes) is woefully insufficient to create something as complex as a human being. The problem is there is only limited transgenerational epigenetic inheritance so it’s hard to assert large amounts of information are stored outside the DNA.
Further, the question arises how is this non-DNA information stored since it’s not easy to localize, in fact, if there is a large amount of information outside the DNA, it is in a form that is NOT localizable, but distributed and so deeply redundant that it provides the ability to self-heal and self-correct for injury and error. If so, in a sense, damage and changes to this information bearing system is not very heritable since bad variation in the non-DNA information source can get repaired and reset, otherwise the organism just dies. In that sense the organism is fundamentally immutable as a form, suggestive of a created kind rather than something that can evolve in the macro-evolutionary sense.
We often hear of genomics, but there are other -omics. There is proteomics, transcritonomics, lectinomics, and who knows what else which fall under the vague heading of epiginomics. If there is an immutable epigenetic kernel for each created kind, then this kernel will resist macro evolvability (like say from bacteria to a eukarya).
There are about 215 cell types in the human, and even supposing an average of a mere 5 developmental stages for each cell type, that’s over a thousand different transcriptomes in the human. The ENCODE consortium tracks only 150 or so transriptomes, and most are for cell in the cancerous stage. Where is the information stored to decide how to dice, splice, rna-edit RNAs, and postranslationally change proteins? ENCODE tracks some of this epiginomic data, but it’s only the tip of the iceberg. In fact, it could be argued each of the 200 trillion cells in an adult human has a slightly different transcriptome and proteome.
What other information storage mechanisms are there aside from DNA? It would have to be fairly fault tolerant so that you can’t knock out large portions of the system, and the information can be re-covered, much like having 100 backup hard-drives. One, and likely not the only information storage device, is implemented by the sugar code.
This link describes how the pharmaceutical industry has invested already 300 million dollars related to the sugar code, and how a mere 3 hexoes has the specificity of about 30 bits ( log2( 10^9) ).
Information carrying capacity of the sugar code
Only God knows how all the information could be stored outside of the DNA complex, but we have hints that for sure there is lots of memory storage capacity outside the DNA. The memory stored through the sugar code might only be one of the many mechanisms through which information is stored in the cell.
Here is another paper:
http://www.ncbi.nlm.nih.gov/pubmed/12223267
Abstract
Analysis of the genome and proteome assumes the focus of attention in efforts to relate biochemical coding with cell functionality. Among other chores in energy metabolism, the talents of carbohydrates to establish a high-density coding system give reason for a paradigmatic shift. The sequence complexity of glycans and glycan-processing enzymes (glycosyltransferases, glycosidases and enzymes introducing substituents such as sulfotransferases), the growing evidence for the importance of glycans from transgenic and knock-out animal models and the correlation of defects in glycosylation with diseases are substantial assets to portray oligosaccharides as code words in their own right. Matching the pace of progress in the work on glycoconjugates, the increasing level of refinement of our knowledge about lectins (definition of this term: carbohydrate-binding proteins, excluding sugar-specific antibodies, receptors of free mono- or disaccharides for transport or chemotaxis and enzymes modifying the bound carbohydrate) epitomizes the sphere of action of the sugar code (functional lectinomics). It encompasses, among other activities, intra- and intercellular transport processes, sensor branches of innate immunity, regulation of cell-cell (matrix) adhesion or migration and positive/negative growth control with implications for differentiation and malignancy. The Q & A approach taken in this review lists a series of arguments in a stepwise manner to make the reader wonder why it is only a rather recent process that the concept of the sugar code has taken root in deciphering the mechanistic versatility of biological information storage and transfer.
“…make the reader wonder why it is only a rather recent process that the concept of the sugar code has taken root …”
The last thing any mechanistic reductionist wants is interacting codes all the way down.
I don’t see how it follows that the organism is “fundamentally immutable as a form”. The organism is relatively stable as a form, able to maintain its organizational closure while still being thermodynamically open to its environment. And I don’t see why autopoiesis is a bar to macroevolution.
KN,
Thanks for you input. Creationists since Linnaeus and Richard Owen suppose there were such things a basic platonic forms that allow some variation (analogous to rectangles being a basic for that allow variation). That is the sense of “immutable” that I was using.
Even more remarkable because 90 percent of it has no function,
Try it. Honestly, do it. Try writing “interacting codes all the way down” in a computer program. Then imagine how hard it would be to create an actual living being like that.
It’s an insane idea. You IDers claim that we can extrapolate out from what we see human designers do but this is the opposite of that. But it’s still evidence for ID huh? No human designer sets out to write code where changing one thing in one layer cascades changes down many “layers”.
I think that subconsciously you’ve realised that “interacting codes all the way down” is actually strong evidence that organisms evolved. Evolution seems likely to generate such networks of interactions, and indeed it seems even further that is the only way you could achieve such. As, otherwise, you’d be able to do so yourself personally. Or someone would have already. EDIT: And so in a bold stroke you claim the idea from the start, hoping nobody will notice the emperor has no clothes.
Sure, there’s plenty of bad “spaghetti” code out there. But that’s not what we’re talking about.
So, go on, point to something in human design and explain how that verifies that Intelligent Design predicts that it’s interacting codes all the way down.
Or just explain why the last thing any mechanistic reductionist wants is interacting codes all the way down, at the very least.
And all the way “down” to what?
I’ve said for some time the way for ID to become a science is to demonstrate that ID is possible. Give us a proof of concept. Show us that some design process other than evolution can create things like regulatory networks.
More correct to say, not as information rich. A heat sink in my computer is information poor, but I wouldn’t say it is functionless.
My tally of repetitive elements in the human DNA is 54% based on FASTA files for HG37 or whatever the latest build is, and about 60% based on C-values. Repetitive elements are not information rich in the Kolmogorov sense, so I don’t think they provide a huge source for ontogenic information, and ontogenic information is more than just protein coding information. A zygote has ontogenic information that a bone cell doesn’t have, so that is strong proof of non-DNA information in the cell.
I agree. But so what?
I’m often criticized by creationists and ID proponents for being a materialist (which I actually am not), and for having a highly mechanistic view of everything (which I don’t actually have). But your own view seems to be that every last detail must be encoded somewhere. That’s far too mechanistic for me. Instead, I suggest that much of the complexity of a biological organism results from adaptive behavior of the development process. If it can be said to depend on information, then a lot of that information seems to come from the development environment, so need not be encoded anywhere.
The Apparently Absent Designer would have to show up to convince some. I respect that, but I still find Design believable despite the difficulty I describe here:
If you don’t find it believable, I don’t fault you for it, I respect your viewpoint, but it’s not for me.
There are other code that implement some sort of memory in the cell such as the histone code and possibly protein isoform codes, isoform codes that are just for individual proteins!
No, it’s more accurate to say that 90 percent of (human) DNA has no function. We know this because it can mutate without consequence.
Sal, you believe so much stupid shit that no one can be surprised at anything you say.
I would say that complex organisms evolve from embryos in the original sense of the word evolve. What you get is the unfurling of cellular automata. Somewhat analogous to the creation of structures by social insects from simple rules.
You can mutate backup drives without consequence, doesn’t mean they are functionless.
The reason ENCODE commands hundreds of millions in budget relative to Dan Graur’s anti-ENCODE cruse is that cancer, diabetes, auto immune, and a host of other diseases are associated with intronic and intergenic regions. GWAS (genome wide association studies) and knockout experiements show stochastic but not deterministic causal relationships.
All the keynote speakers at ENCODE 2015 and many of the other presenters pointed out the importance of intergenic and epiginomic information. Even the repetitive elments have role, and they don’t just store information in the linear ordering of ACTG. For example teleomeres “TTAGGG” repeats possess information in the way they knot. The repetitive elements may have 3D spatial functionality, not the least of which influences encahncers that may be a million bases away from the gene they regulate, but are spatially close in terms of 3D topology because DNA coils.
But all this may be moot if the epigenome is information rich, which seems to be the case since the epiginomic state is highly important to the fate of cells being healthy or cancerous or whatever.
I guess I’ve run out of surprises then. 🙂
What is the function of backup drives if scrambling their content makes no difference?
You ran out of surprises 10 years ago.
How do you know it makes no difference. Scrambled content would obviously reduce the ability to self-heal or resist certain disorders. The ENCODE researches are seeing that — people who actually do work in medical research rather than arm-chair evolutionary ideologues like Graur.
Besides, the ENCODE epigenetic database and other epigenetic databases will run over Graur’s insinuation that the cell contains little information.
Hundreds of millions of dollars are being put into the research of information storage implemented by the Sugar Code, the Histone Code, the transcriptome, the proteome and who knows what else. The money is invested because it furthers biotech and medical technology. These guys, though mostly believing evolutionary theory, could care less about Graur’s whining that there can’t be that much integrated and complex information in the life.
If the human epigenome stores tera giga bytes or more of ontogenic information in the zygote, Graur’s whinings over DNA are going to be moot in the end because there is much more to information storage than DNA.
Because it’s not conserved. Mutations accumulate without affecting viability.
Epigenetic changes disappear over several generations. They do not get encoded in the genome.
I’m not really sure if I agree with the notion that there is information outside the genome. We could say that the expression of the genome creates complexity which is the foundation for yet more complexity but we need to remember that DNA is at the base. So info is stored in the glycosylations of membrane proteins but the glycosyltranferases that add the sugars are coded for in the genome, expressed by the genome and the ER and Golgi in which they’re active are maintained by the genome.
The way I see it is that the information is the genome is present in ‘layers’ or ‘dimensions’ The transcriptional networks are a layer, the splicing regulation, and of course epigenetic regulation are all distinct layers of information and complexity. Even the functionality of proteins contains layers of info.
Perhaps this partially answers the paradox that Sal brought up.
Information is a metaphor. It is a kind of map. We study mostly genomic DNA because it is the least conserved carrier of variations. Mutations in mitochondrial DNA are much more likely to be debilitating.
It’s interesting that creationists like Kirk Durston are big on genetic load and on the degradation of DNA, but fail to notice that change occurs at different rates in different parts of the genome. Protein coding stretches of DNA are more conserved than non-coding stretches.
But with a few exceptions, most living things have vast swaths of DNA that tolerate mutations without affecting viability.
More correct to say lacking in any information relevant to the organism’s survival, reproduction or health.
I know and work with many people in medical genetic research. They were as annoyed by the “80% functional” nonsense as the evolutionary biologists.
As far as we know, all of that information — all that is inherited, at least — is ultimately encoded in DNA. Taken together, the DNA that holds the information constitutes about 10% of the human genome; at least that’s the best estimate to come from the ENCODE studies.
Why?
Nobody ever answers your question, Petrushka. It’s like it’s invisible.
I am invisible, but only when no one is looking.
Sandwalk has some relevant discussions going.
http://sandwalk.blogspot.com/2015/07/kirk-durston-appears-on-uncommon.html
http://sandwalk.blogspot.com/2015/07/john-avise-doesnt-understand-central.html
http://sandwalk.blogspot.com/2015/06/junk-dna-is-so-last-century.html
Larry Moran has offered up a thousand dollars bet to any credentialed biologist or biochemist who will debate him on junk DNA. Presumably to be juried by other biologists. Larry has a rather dim view of ENCODE. A view shared by most evolutionary biologists.
http://sandwalk.blogspot.com/2015/07/the-fuzzy-thinking-of-john-parrington.html?showComment=1436179477511#c5578522711139303732
I understand the concept perfectly well; what I don’t understand is why you (or anyone) thinks that is a correct description of biological organization.
Linnaeus and Owen were thinking about biological form before we knew much of anything about how organisms maintain a far-from-equilibrium thermodynamic relation with flows of matter and energy in their environment while maintaining their structural coherence. (And if memory serves, they were thinking about biological form in terms of anatomy; they didn’t even know that much about physiology, morphology, or embryology.)
Now that we have some pretty good models of how autopoeisis is achieved, I don’t see the appeal of a Platonic, creationist conception of biological form, and I certainly don’t see how autopoiesis, as a theory of biological form (indeed, as a theory of biological teleology), is incompatible with macroevolution.
stcordova,
It would surprise me if you went back to your YEC thread and addressed the refutations of your ridiculous claims instead of disappearing for a few days and then starting a new thread as though nothing had happened.
What won’t surprise me is for your claims to be equally thrashed in this thread and for you to come back in a month or two with new nonsense.
Hi Salvador,
Could you summarize the main points of the OP?
I agree that not all the needed information is in the DNA.
I disagree that the “missing information” must necessarily exist somewhere else.
Surely there are means to construct things absent complete information.
If course, if such a means does exist for cells and organisms that’s just another aspect of the mystery that is life.
Or not. (See, I noticed your post!)
Kirk posted his information argument over at UD a while back and my first criticism of it was that it claimed that all the information was in the DNA. I was accused by others of taking what he wrote too literally (haha – imagine that). But Kirk later returned and verified that I had understood him correctly, that it all comes back to the DNA.
And, “in science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to prhenology than to physics.” Since when has evolutionary theory made substantial contribution to medical science except to say some organism look similar to another so lets study similar organisms. Similarity was known by creationists in Linnaeus’s time, for that matter, for who knows how far back!
Molecular and computational biologists who actually study diseases related to non-coding DNA are the ones who should be making the call, not evolutionary phrenologists who frankly can’t decide on the non-Coding DNA issue either!
Most ENCODE researchers who run labs could care less if the figure is 10,20,30,40…100% functional in whatever definition Moran wants to use for functional. They just know diseases and dysfunciton often appear associated intergenic and intronic regions, and hence they collect huge databases of genetic and EPIGINOMIC dtata that is tied to DNA, EPIGINOMIC which includes the following marks on non-coding DNA:
http://www.nature.com/nature/2015/180215/full/nature14310.html
These marks on non-coding DNA are important to health.
Larry wants to bet $1000? Laughable. The ENCODE consortium has already been awared hundreds of millions. The real jury, the medical community, has decided in favor of supporting ENCODE research, and money has been put where the jury’s mouth is.
Speaking of EPIGINOMIC and the non-DNA information, methylation marks can appear on non-Coding DNA, epecially repetitive elements. It appears then the repetive DNA can act as a blank memory storage unit for any sort of navigational machinery that utilizes methylation marks! No wonder repetitive DNA seems to be implicated in disease, it’s practically a roadway for non-DNA regulatory information!
What did I say about evolutionary theory being next to worthless for medical science. In fact, given its track record, it’s a distraction at best, harmful at worst.
Larry Moran, a biochemist ought to know better than to be so presumptuous.
The necessary transitionals would not be functional enough to live. If there were common descent, it would have to be hopeful monster type changes. As Gould said, “what good is half a wing?”. At the biochemical, nano-level the difficulties are even more pronounced.
For example the sugar code in bacteria is different than in humans. Linguistic changes to the norms of how a machine coding system work are catastrophic to the machine. One can’t change the grammatical structure for machine languages without catastrophe. That’s why a creature with one coding system is immutable since substantive violations of its grammar are lethal.
Dear Mathgrrl,
Is your empty taunt the best you can do? No technical refutation of the Surgar code and its information carrying capacity? How about the information implemented through the other -omes?
Want to trash the OP, go right ahead. I’m listening.
And I’m not done with the YEC threads. I’ll revisit them.
If I win this exchange:
Sal: 1
Mathgrrl: 0
As far as me being trashed on threads, were you referring to my assertion 500 fair coins 100% heads is not consistent with the physics of fair coins and the binomial distribution? Or how about me quoting NIST information that indicated the dimensionless units of entropy. We know which side got trashed on that one. 🙂
In the meantime, try to refute the OP if you’re able.
stcordova,
How’s young cosmos / creation evolutionary university going? You have rebooted these things a few times, perhaps that was Patrick’s point?
Here is a book that indicates 3 types of memory in the cell, of which DNA is only 1 kind of memory:
http://www.ncbi.nlm.nih.gov/books/NBK28320/
This shows ontogenic information cannot be solely contained in the DNA.
Here is one example of evidence that damage to the cytoplasm can create damage to the DNA:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC21799/
What this means is there is some subtle loophole to the central dogma. The structure of proteins is governed by DNA, but DNA can be accidentally altered by failures in coded protein machinery.
That means the cytosol contains technology highly important to life, and in that sense it is information bearing even if the information is hard-wired.
By hard-wired, I mean in the sense that a car’s engine (minus the car computer), may not have information in the sense of reading bits and bytes from memory, but it has technology in the composition of its parts to make the engine run.
The human body has around 200 trillion cells, and if we include even an average of 5 developmental stages for each cell, that’s about 1 quadrillion separate transcriptomes that must be managed and coordinated expressed in uncertain developmental environments.
This is more complex than just running a “for loop” in a computer program because environmental uncertainties don’t allow for a deterministic path.
Hence the 800 megabytes of DNA information seems insufficient to create a human, there is probably a lot of hard-wired, deeply redundant technology that provides ontogenic information to express and manage hundreds of trillions of cells in various stages of development.
DNA may influence all the proteins, but it certainly doesn’t define their final dispositions and form.
Hey Mathgrrl, Rich is giving you an off topic. You want to bite so you can avoid addressing the OP? 🙂
stcordova,
It was addressed to you Sal. Look at it this way, use Laplace’d rule of succession based on your posting history (no other knowledge is needed) to estimate your chances of being right on this one (the requisite knowledge I don’t have) – what are the odds you’re right? I’m not trying to be mean, but there is a strong pattern, no?
Well, it’s absolutely key to our understanding of many pathological processes, including infections (viruses and bacteria) and the immune system, and the way that infectious pathogens change in virulence over time, including in response to our attempts to combat them.
It’s also at the heart of developmental biology, and thus informs our understanding of developmental disorders.
It is also key to understanding why so many conditions are polygeneic – why the vast majority of people with a “risk” allele do not have the condition it is a “risk” for. Our ability to use this understanding is in its infancy (but then so is GWAS), but already it is helping us understand the dimensional nature of, for example, heritable mental disorders.
To be honest, it’s hard for me to think of a branch of medicine to which evolutionary theory is completely irrelevant. And yes, finding good animal models is one of the most important.
stcordova,
That’s not my handle here, Sal. You wouldn’t be one of those reprehensible doxxers, would you?
Hardly an empty taunt. It’s an observation of your behavior over the years. You historically have failed to engage with substantive criticisms of your positions and frequently leave the discussion for a period of time before coming back and starting another topic as if nothing had happened. The YEC thread is just one example.
This is why I do not usually respond to you — I do not consider you intellectually honest. You might be posting in good faith in the sense of believing the nonsense you say, but I believe based on your behavior that you are interested only in buttressing your faith, not learning anything about the topics you discuss.
No, I’m referring to your ridiculous claims about the age of the earth and the age of life. Those have been soundly refuted for decades, yet you utterly fail to address those refutations.
You appear to be suggesting there may be an additional heritable system of storing genetic information other than DNA. With DNA we know how it is present in all nucleated cells in the body, having replicated from the original zygote, we know how the information is read off into RNA and protein and how it is passed on to offspring via gametes.
Other than the theoretical idea, what have you in the way of an information storage and retrieval system involving carbohydrates? What’s to refute?
So go write, peer review and publish a paper on it. Or stick it in a blog comment, whatever you think will achieve the most….
Evolutionary biology — especially the fact of common descent — makes substantial contributions to biomedical research all the time. We use it to determine which allele is ancestral (key for detecting positive selection), for estimating and correcting for local mutation rates, for estimating the correlation of mutation rates, for detecting functional elements in DNA. Our research institute has spent and is still spending large amounts of money on comparative genomics, not because we’re interested in evolutionary biology but because it’s useful for our mission of biomedical research.
How convenient: I’m a computational biologist who actually studies diseases (some related to noncoding DNA — we don’t know until we look). I’m here to tell you that you have no idea what you’re talking about.
Uh huh. What you seem to have missed, though, is the point of ENCODE: to identify the small regions of noncoding DNA that are functionally important in different tissues. Simply declaring all introns to be functional, for example, because they’re transcribed is utterly useless.
Of course we (or most of us) support ENCODE. I’m not disagreeing with the existence of ENCODE; I’m disagreeing with your own idiosyncratic and quite implausible suggestion in this thread. You might note, by the way, that the medical community — the real jury — has also spent hundreds of millions of dollars on comparative genome sequencing of lots of other organisms, based on evolutionary biology. Are you prepared to accept their verdict?
Something true.
Something you made up.
Learn to distinguish the two.
Of course ontogenic information is not solely contained in DNA, in differentiated tissue. That’s why biologists have been studying epigenetics for decades. You keep stating facts that every biologist knows, rather than providing any support for your novel hypothesis.
The fact that radiation can produce mutagenic chemicals has nothing to do with your claim in the OP — or with the central dogma. It also has nothing to do with “failures in coded protein machinery”. Your introduction of it here is baffling.
How many different cell types are there among the 200 trillion (or more likely, 40 trillion) cells?
Most developmental paths are deterministic: you don’t develop pancreatic islet cells in your heart. And once a cell’s fate is set, its transcriptome is indeed deterministic. So the bit about trillions of cells is irrelevant.
stcordova,
Wha? Are zygotes derived from bone cells? Or is it the other way round?
This article shows it is an accepted paradigm that epigenetic memory on the DNA strand is readable and writable and even potentially re-programmable!
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662891/
You’re the one making stuff up by imply that epigenetic memory on the DNA doesn’t exist.
http://www.ncbi.nlm.nih.gov/books/NBK28320/
Nuclear Memeory: composed of DNA, methylation marks, histone modifications, etc.
Cytoplasmic memory: memory implemented by sugar code, and who knows what else
Autocrine memory: still more memory outside cells in a multicellular environment
There is more than just the DNA ACGTs to provide information and technology to make a human being.