Scientists discover double meaning in genetic code

Dec 12, 2013

Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of and of medicine, made the discovery. The findings are reported in the Dec. 13 issue of Science. The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for are stored in the human genome.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

"For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made," said Stamatoyannopoulos. "Now we know that this basic assumption about reading the missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways."

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient's genome and will open new doors to the diagnosis and treatment of disease.

"The fact that the can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting programs or even both mechanisms simultaneously," said Stamatoyannopoulos.

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Zorlont3
1.6 / 5 (19) Dec 12, 2013
Seems to me like this is just more and more evidence of god. I mean, you can only have so many pieces falling together before it becomes a little fishy.

We have evolution. Which describes what happened after all the nearly impossible stuff happened. Then we have some sorts of chemistry to describe what happened before any of the hard stuff happened.

Spend a few million years watching random bricks fall together, until they make a perfect square.

Close your eyes for a few billion years and when you open them, skyscraper!

Makes more sense to me that something stopped by and glued us together. lol
scottfos
3.5 / 5 (13) Dec 12, 2013
Zor, it must be nice that no matter what you learn or don't learn it merely reinforces your preconceived notions. almost makes one wonder, why bother learning anything at all? which, of course, explains a lot about so many of your brethren....

back on topic, this is very cool. codons did a lot to explain why there is so much DNA similarity between humans, chimps, mice and canines; if this work on duons pans out it will open a lot of new opportunities.
11791
3.7 / 5 (3) Dec 12, 2013
Expect the discoveriers of duons to win the Nobel prize if their interpretation of the data pans out. They call them duons not gluons zorlont3!
AeroSR71
3.9 / 5 (7) Dec 12, 2013
This isn't evidence of God. That just brings up more questions, such as, which God? After all, humanity's made up thousands of deity's over the years.

More on-topic, does anyone know why DNA has 64 letters? Or, said differently, why did evolution choose 4 base molecules (nucleotides)? Is there something about information that works best in bases of 2? There must be some underlying effect that makes symmetry appealing?
Whydening Gyre
1.8 / 5 (5) Dec 12, 2013
Is there a parallel to be drawn in relation to machine language and higher coding methodologies?
CassusVas
5 / 5 (10) Dec 13, 2013
@AeroSR71:

DNA has 64 possible combinations per codon (4^3) because there are 21 normal/abundant amino acids. Basically, only 2 nucleotides per codon would only be able to code for 16 amino acids (4^2), so life went one further to 3 per codon to cover all the amino acids that are regularly used to make proteins/peptides. Also, the fact that there are 64 possible combinations used for only 21 normal amino acids allows for several different sequences/codons to be used for especially important amino acids (to give the system some flexibility/robustness against mutation, etc). Also, then some of these codons can be used for start and stop codons to signal to the cellular machinery what the start or stopping point of a peptide/protein is.
JVK
1 / 5 (3) Dec 13, 2013
CassusVas: You seem likely to know about glycine. If so, please tell me the significance of the only achiral amino acid. Thanks.

James V. Kohl
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.socioa...53/27989
JVK
1.6 / 5 (7) Dec 13, 2013
BTW: This is evidence of God. "The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution." It attests to the biological fact that ecological adaptations in every are nutrient-dependent and pheromone-controlled via epigenetic effects on amino acid substitutions. Nothing random; nothing but diseases and disorders caused by mutations. The evidence unequivocally refutes the idea of mutation-initiated natural selection, or mutation-driven evolution, which is the new way to explain how organismal complexity "just happens" since the biophysical constraints on adaptations ensure mutations are not naturally selected. In fact, they're not even fixed in the DNA of the organized genome of any species -- so they can't be selected as the population geneticists have led people to believe. http://www.scienc...abstract
Jaeherys
3.7 / 5 (3) Dec 13, 2013
This summary does not accurately present the data in the original publication. The researchers found that specific trinucleotide sequences (codons), aprx. 15% of them, correlate to specific transcription factor (TF) binding sites in coding and noncoding regions. Basically, certain codons were found to have statistically increased TF binding to them more often than others. Together this suggests a physical basis for codon bias as TF binding selects for these specific sequences. It also suggests a mechanism of codon bias amongst genetically similar species like mice.

Although interesting, I find it not as important as snRNA reguation via RNAi or antisense snRNA mRNA interference. These snRNA can be found in noncoding regions of genes and DNA which shows multiple levels of regulation on a more genome wide scale and gene scale as specific miRNA are produced from introns from both 5p and 3p transcripts.
JVK
2.6 / 5 (5) Dec 13, 2013
I think it is interesting that no one has linked changes in the microRNA/messenger RNA balance to the duons and further downstream from epigenetic effects to alternative splicings and the diversity of cell types in different species that are detailed in the context of amino acid substitutions.
Torbjorn_Larsson_OM
4 / 5 (4) Dec 13, 2013
Contrary to what the antiscience creationist and pheromonist trolls claims, codon bias has been known since the 80's and doesn't support magic and/or snakeoil. [ http://en.wikiped...age_bias ]

The extension of such a "code" to transcription isn't surprising, nor the main mcehanism for regulation. As the perspective article says: "This "binding" code joins other "regulatory" codes that govern chromatin organization (3), enhancers (5, 6), mRNA structure (7), mRNA splicing (3), microRNA target sites (6, 8), translational efficiency (9), and cotranslational folding (10), all of which have been proposed to constrain codon choice, and thus protein evolution (see the figure)." [ http://www.scienc....summary ]
TheGhostofOtto1923
3.7 / 5 (6) Dec 13, 2013
This isn't evidence of God. That just brings up more questions, such as, which God? After all, humanity's made up thousands of deity's over the years.

More on-topic, does anyone know why DNA has 64 letters?
Well obviously it is a direct reference to Isiah 64 wherein we find

"8 Yet you, Lord, are our Father.
We are the clay, you are the potter;
we are all the work of your hand."

-So yea unto you, the hand of god is seen in the bowels of man once again. For written_it_is.

For yet more testimony see the outrageous crap posted by JVK.

JVK, there might be some god or other that is responsible for whatever it is you are talking about, but it is obviously not the god who said there was a flood (there wasnt), or an exodus (never happened), or a joshuan genocide (nope) or some great solomon/david kingdoms somewhere (uh uh) or a town called nazareth during the time of jesus (dirt in the desert).

THAT god is neither omnipotent nor omniscient nor honest nor good nor real. Amen.
Whydening Gyre
2 / 5 (4) Dec 13, 2013
I have a sneaky feeling that a third level of biological instruction will be divined from duon research.
Whydening Gyre
2 / 5 (4) Dec 13, 2013
Correct me if I'm wrong, but -
Environmental change can drive nutrient change, which in turn would drive cell adaptation to a new set or ratio of nutrients). Surely those changes aren't spot on right in the beginning. A little trial and error (which nature/evolution does a lot of) - and the resulting biological species that survives is a result of "mutating" most propitiously.
Doesn't have to be a large change to be considered a mutation, does it?
JVK
1.8 / 5 (5) Dec 13, 2013
Climate change -> diet change -> ecological variation -> epigenetically-effected adaptations (sans mutations).

If Climate change -> diet change -> ecological variation -> AGAIN, you get more adaptations (sans mutations)

What the study results reported here tell us is that transcription and gene expression are as flexible as they must be to allow for adaptations when climate change precipitates a dietary change due to the ecological variation that is responsible for adaptations via the de novo creation of olfactory receptor genes, de novo creation of species-specific blends of pheromones, and de novo creation of physical structures like teeth or eyes or whatever, which are all the result of alternative splicings and amino acid substitutions in all species.

The amino acid substitutions are not mutations and mutation-initiated natural selection defies the biophysical constraints that clearly facilitate ecological adaptations, not mutations.
Whydening Gyre
2 / 5 (4) Dec 13, 2013
Okay...:-) So it appears I must change my definition of mutation...
Jaeherys
3.9 / 5 (7) Dec 14, 2013
No, I don't think you need to change your definition of mutation unless it doesn't involve environmentally influenced random mutation. Excluding all DNA damage based mutation or major errors during replication, like large regions of chromosomes being shifted around or connected together in odd ways, the rates of SNPs are well characterized. If my memory holds, i think its about every 1 in a billion nucleotides are misinserted during polymerization and this number can be influenced by the environment. For example, unbalanced nucelotide ratios can increase misinsertions and lead to more single nucleotide polymorphisms. So in essence, poor environments can increase mutational rates and the probability of increasing fitness. For example, at my lab I am trying to produce cells that are resistant to low oxygen and nutrient environments in cells that are normally extremely fussy about where they live. To do this, I basically culture cells in these environments, in a stepwise fashion.
Jaeherys
4.2 / 5 (5) Dec 14, 2013
Overtime I produce colonies that are able to proliferate better in these environments and then i again decrease oxygen levels and nutrient levels. Along the way you'll see cells that mutate horribly with things like multinucleation, polysomy, aberrant mitosis or cytokinesis, etc, etc. Another very common change is syncytialization where cells basically fuse parts of their membranes or form tight junctions with neighboring cells to produce multinucleated cells. These syncytialized cells can contain as many as 10-20 nuclei sometimes! You also see large changes in morphology where cells change the way they contact each other, typically they form more tight junctions, possibly as a way to reduce surface area contact with unfit environments as a means to stabilize internal levels of ions or interaction with extracellular signal ligands. After i produce cells that can proliferate to some extent in the desired environment, you select for colonies that door very well and very poorly,
Jaeherys
4.2 / 5 (5) Dec 14, 2013
generally by choosing either colonies that grow quickly or spread out very quickly and conversely, by choosing colonies that dont grow quickly and dont spread out. In this way, i have done two things: produced cell lines the differ from their parent cells and quantification of gene expression or gene sequence differences between the parent and mutant cell line. This is typical when you want to see what is the difference between cells that can and cant do something. But the message here is this, mutation happens via multiple pathways and doesnt always involve DNA mutation but changes in epigenetic tags, gene expression, or environmental-dependent functional variances in proteins. But to say that DNA mutations that affect amino acid sequences or regulatory sequences is not a part of evolution is severely misguided. We consistently see DNA changes via mutation that affect organismal fitness as well as routinely use these techniques to mutate cells in a direction we want them to go.
JVK
2 / 5 (5) Dec 14, 2013
"We consistently see DNA changes via mutation that affect organismal fitness as well as routinely use these techniques to mutate cells in a direction we want them to go."

What prevents you from recognizing that those changes are nutrient-dependent and pheromone-controlled? Is it possibly because you don't know the difference between a mutation and an adaptation? Are you, for example, Richard Lenski? If you're anyone else and don't change your definition of a mutation to include biophysical constraints on adaptations associated with evolution, biophysicists, chemists, and biologists will continue laughing at you -- if only behind your back. Is that why you participate anonymously here?

If I were you, I wouldn't want anyone to known that I had actually published anything on mutations theory that ignored the fact that mutations cannot cause adaptations, cannot be selected et al.

Jaeherys
3.7 / 5 (6) Dec 14, 2013
What prevents you from recognizing that those changes are nutrient-dependent and pheromone-controlled?


Nutrient levels do affect mutation rates but as for pheromone-controlled, I'm not sure I follow. What is an example of a mechanism that directly leads to mutation and adaptation, and without pheromone involvement, cannot produce these results? I am genuinely interested as cell signalling is quite obviously vital in multicellular organisms and could quite possibly affect organismal fitness.

What I fail to conclude is that mutation and adaptation are not related. There is ample evidence showing that mutation may cause changes in phenotype that can manifest as an adaptation increasing fitness.

Is it not a bit presumptuous to assume that nutrients and pheromones are the only factors controlling the evolution of organisms? Especially considering the genetic changes that occur in constant nutrient environments in vitro when just left long enough on their own.
Jaeherys
3.4 / 5 (5) Dec 14, 2013
Furthermore, a beneficial genetic change can be selected for, especially when this change produces a phenotype that overwhelmingly out competes other phenotypes. For instance, if a population was exposed to disease X, which has a fatality rate of 90%, and 5% of people in this population predominately express a mutant isoform of a protein that abolishes this diseases mechanism of transmission, how is it that this mutation does not cause an adaptation? Moreover, if this mutation originated via chemically induced DNA damage and erroneous repair, does that not suggest other factors that may influence the course of evolution on a larger scale?

I just don't see how pheromones and nutrients are the sole causes of adaptation. Why is it that some species remain predominantly constant over millions of years even in the presence of varying nutrient levels and pheromones? What I see is the environment not producing any selective pressure and deleterious mutations being selected against.
jxaxmxixn
3 / 5 (3) Dec 14, 2013
Seems to me like this is just more and more evidence of god. I mean, you can only have so many pieces falling together before it becomes a little fishy.

We have evolution. Which describes what happened after all the nearly impossible stuff happened. Then we have some sorts of chemistry to describe what happened before any of the hard stuff happened.

Spend a few million years watching random bricks fall together, until they make a perfect square.

Close your eyes for a few billion years and when you open them, skyscraper!

Makes more sense to me that something stopped by and glued us together. lol


Obviously you have not even the most fundamental clue on how chemistry works. You should probably try to learn how atoms are formed, and then how atoms connect together to form all of the simple to complex molecules that make up our planet universe.
The logic you've tried to use here (buildings building themselves, etc...) is NOT how evolution happens! Try reading a science book!
GuruShabu
5 / 5 (4) Dec 14, 2013
It is unbelievable how much lessons on genetics, physics, cosmology you can get for free here!
JVK
1.7 / 5 (6) Dec 14, 2013
More free stuff:

Two H-bonds are critical for slow inactivation of Kv channels: one that confers stability within an individual subunit (the Trp434–Asp447 interaction), and a second that stabilizes the relative orientation of two adjacent subunits (the Tyr445–Thr439 interaction).

If this stability, which is probably important to the stability of life itself, results from randomness that somehow enables the thermodynamics of intercellular signalling, stochastic gene expression, and the amino acid substitutions that result in organism-level thermoregulation, which differentiates individuals and species from all other individuals and species via genetically predisposed differences in antigenic properties like those determined by a single amino acid substitution in the human influenza virus, the atheists are right and they could probably prove it.

Alternatively, the explanation is Creation, which atheists say Creationists can't prove. I believe that someone's bound to be embarrassed.
JVK
1.8 / 5 (5) Dec 14, 2013
Jaeherys should already be embarrassed.

"I just don't see how pheromones and nutrients are the sole causes of adaptation."

Nutrients fuel the thermodynamics of intercellular signaling; species-specific pheromones control the physiology of reproduction in species from microbes to man.

What other causes of ecological adaptation might involve mutations? Is there a model of ecological, social, neurogenic, and socio-cognitive niche construction for that?
Jaeherys
4.3 / 5 (6) Dec 15, 2013
I'm not embarrassed to discuss well documented phenomena but using creationism as a way to try and disprove evolution is just silly. How can you explain such things as body plan progression, tissue homology, cell homology, and gene and protein homology between species ranging from microbes to mammals? All these things together show considerable evidence of evolution through mutation and natural selection. To add on top of that fossil records and behavioral similarities further confirms that we are all at the very least related and evolved. We most likely know just a small part of the picture but that small part was no easy feat. And by no means is that small part inconsequential, it has taken decades of hard work fighting irrational thought and human bias but we are finally at a stage where people are beginning to see, we aren't exceptional among organisms, we are just another unique piece of the puzzle. Unfortunately, all the pieces are *almost* incomprehensibly complex.
JVK
2.3 / 5 (3) Dec 15, 2013
The pieces are not incomprehensibly complex; they just do not fit the picture of mutation-driven natural selection. You need only look at all three articles in Science Magazine this week that collectively show how nutrient-dependent pheromone-controlled transcription and gene expression enable amino acid substitutions that differentiate cell types (cave fish eyes), individuals (immune systems) and species morphology.

Otherwise, you're going to keep thinking in terms of mutations instead of de novo creation of olfactory receptor genes, de novo creation of species-specific blends of pheromones and de novo creation of nutrient-dependent physical features like eyes or other morphological characteristics in cells from microbes to man.

Simply put, you will continue to think like an uninformed theorist who attributes the complexity of ecological, social, neurogenic, and socio-cognitive niche construction to mutations and natural selection instead of ecological variation and food choice.
Jaeherys
4.2 / 5 (5) Dec 15, 2013
Ok, let's try something. If you tell me the mechanism for this de novo creation of olfactory receptors I will go into my lab, do the experiment, and tell you if I see de novo creation of new genes; I'll even repeat it multiple times. You tell me the hormone to treat with or experimental conditions and I'll do it. I have access to many cell types from mice, zebra fish, hamster, rabbit, and humans or some compounds to differentiate into multiple placental cell types. And don't give me some bs about needing a whole mammal :P! Furthermore, if it does work and I can validate it id be willing to share with you the raw data.
JVK
2 / 5 (4) Dec 15, 2013
Thanks for the offer. The experiments have already been done, however.

"We have shown here that the activity-dependent replacement of canonical H2B with H2BE, an olfactory-specific histone variant, has a direct impact on the gene expression and life span of olfactory sensory neurons. These findings uncover a novel mechanism by which the sensory experience of a neuron is recorded within its chromatin to affect its transcriptional program and longevity." http://elife.elif...1/e00070

Lots more evidence of cause and effect across species.

How do you account for your lack of knowledge in the context of ecological variation that obviously is linked from flies to amino acid substitutions in receptors in human olfactory receptor neurons as well? I think you may have been taught too much about theory, without asking if the theory was supported by experimental evidence. Thus like others, you think experimental evidence is a Creationist thing. To me, it's Science.
Jaeherys
4 / 5 (4) Dec 15, 2013
Ok, I read the paper, albeit quickly, and what I get out of it is a process for enhancement of neuronal populations to commonly activated olfactory receptors. You have a population of neurons that deferentially express ORs and over time, ORs on neurons that are consistently activated have increased longevity and neurons with ORs that are inactive, increase H2BE expression and have reduced longevity, freeing space for neurons that contain ORs that are active. This mechanism is similar to synaptogenesis in the developing brain where there are large amounts of arborization which leads to pruning of inactive synapses. The extension of this mechanism to olfactory epithelium would be expected, as these neurons exhibit a behaviour similar to the developing brain but without terminal differentiation. What i see here is cells doing what they always do, respond to environmental queues and this H2BE variant is suggestive of a major shift in transcription.
Jaeherys
4 / 5 (4) Dec 15, 2013
I dont see any de novo gene creation here.

I mostly work in cell biology and gene regulation and not genetics or evolution, so i cant say either way if this is evidence for or against your theory. Also, considering how little change there is between the histone variants, dont you find that indicative of mutation? Such small genetic changes produce such a huge change in phenotype and ultimately the whole olfactory system!

And on a complete side note, my lab also studies cyclin G2 regulation and function in human ovarian cancer. Due to its unconventional nature, it appears to be a negative regulator of cell survival due to stress, DNA damage, etc. This H2BE-mediated reduction of MOE longevity is intriguing as glial cells seem to show CG2-mediated apoptosis. So I may have found another cell type to study in a more stable model system. So thanks for linking that paper!
JVK
2.3 / 5 (3) Dec 15, 2013
Do you ever see any de novo gene creation? If not, how is it that increasing organismal complexity "just happens." Have you noticed any connection between obesity and cell types associated with cancers? Do you think nutrient uptake and amino acid substitutions have anything to do with typical and atypical cell type morphology?

I often wonder at how much different specialized areas of research contribute to the inability to see the forest for the trees. Most people are incapable of thinking in terms of modeling developmental changes across species. If they did, they couldn't possibly continue thinking in terms of mutation-driven evolution. They might never be capable of thinking in terms of

"Nutrient-dependent/pheromone-controlled adaptive evolution" http://www.socioa...53/27989

But if they weren't so specialized, at least they might start to think.
11791
1 / 5 (1) Dec 16, 2013
Hi SR 71 it evolved that way. one to one base pairing was able to reproduce itself. thats all. it took off after that. other combinations were possible but base pairing got a head start on other possible types of molecular information storage.
JinXer
3.4 / 5 (5) Dec 16, 2013
The Christian God is a paradox... their assertion is that he is both Eternal and Omnipotent. Which cannot be. Eternal means that he has always existed and shall always exist, he cannot not exist. Omnipotent means that no action is beyond his abilities. This means that if he so chose, for reasons beyond our understanding, decided to destroy himself he would have the power to do so, and would cease to exist. Well then he's not Eternal. And if he is in fact Eternal then he is not Omnipotent. God is broken.
JVK
3 / 5 (2) Dec 16, 2013
11791

If you have the source for that information, it might benefit others. I certainly would like to examine it, since I have never before heard that only the reproduction of one base pair was required to kick-start all the other types of storage. I'm reminded,however of an article by "Uncle Al Schwartz" about "The Power of Two" which might help to place the first base pairing in context.
SURFIN85
1 / 5 (1) Dec 17, 2013
The four nucleotides make more combinations than possible proteins and all proteins thus made were assumed to be functionally equivalent. But what was discovered was that, in the intermediate step between the nucleotide combination and the making of the protein, the nucleotide combinations have to be ferried across the internal landscape of the inside of the cell. And different combinations of the same codon triads have different energetic properties in a fluid medium- some can travel faster, and some slower. So this gives the genetic code added complexity and gives the cell's organization a way to regulate the cellular processes by controlling the rate of protein synthesis. The observation was that, in different environments, the genes were regulated for more conservative synthesis in deprived environments and quicker, more responsive synthesis in abundant mediums. In combination with epigenetic modification, a low-level gene regulating function is inherent in the system.
Whydening Gyre
1 / 5 (1) Dec 17, 2013
Molecular algorithms?
JVK
1 / 5 (1) Dec 17, 2013
Thanks SURFIN85. I was beginning to think that no one could put this is terms anyone else might comprehend so that the terms could be placed into the context of nutrient-dependent pheromone-controlled conserved molecular mechanisms of amino acid substitutions in species from microbes to man. Please consider commenting to the Science Magazine site. So far, I think you are attesting to the biophysical constraints of thermodynamically controlled intercellular signaling (i.e., an inherent low-level gene regulating function). Clearly, that would be energy-dependent and in my model the energy comes from nutrient uptake.

Energy expenditure is controlled by the feedback of chemical signals that are typically called pheromones.

I'd love to see a followup to my comment here: http://comments.s....1243490 or to the summary of the four Science articles I posted to my domain: http://pheromones...s-redux/
JVK
not rated yet Dec 17, 2013
Jaeherys; SURFIN85; Whydening Gyre:

"H2be may be subject to different post-translational modifications than canonical H2b. Indeed, Santoro and Dulac show that lysine 5 of H2be is not acetylated or methylated, unlike what happens with canonical H2b, and that the level of the these post-translational modifications in olfactory sensory neurons varies with H2be levels. Since these modifications have been positively correlated with transcription (Wang et al., 2008) it is intriguing to think that global transcription is less efficient in neurons with high H2be levels."

One of the authors of the piece I just quoted got my comments on it blocked and then they were removed. To me it was clear that I "nailed" the process of de novo creation of olfactory receptor genes via epigenetic effects of chemical signals from the bottom up that must result in organism-level thermoregulation, which is epigenetically controlled from the top down.

If I was wrong, discussion might have ensued.
Zephir_fan
Dec 17, 2013
This comment has been removed by a moderator.
JVK
1 / 5 (1) Dec 17, 2013
Yes;This:

http://www.jbc.or...abstract

Kohen's group clearly links E. coli to Homo sapiens via amino acid substitutions that are conserved. They report that "…a four amino acid insertion (PEKN) was introduced early in the enzyme's evolution and is highly conserved in higher organisms." Conserved molecular mechanisms in species from microbes to man link amino acid substitutions that are conserved to other amino acid substitutions that differentiate cell types, individuals and species. It is not surprising to see a report on this research that states "At the molecular level, evolution reshaped some of the enzymes that help complete chemical processes — such as converting food into energy — in humans and all other life forms." The conversion of food into energy is a condition of life.

Mutations perturb the dynamic constraints of protein folding. They do not reshape enzymes to help convert food into energy that enables beneficial amino acid substitutions
JVK
1 / 5 (1) Dec 17, 2013
"We found that a brief pulse of the ELT-7 GATA transcription factor activates intestine-specific gene expression in diverse non-intestinal cells."

Of course this suggests that the balance of transcription and gene expression must be finely tuned, which argues against mutation-driven evolution since mutations perturb intercellular signaling and stochastic gene expression.

A brief pulse of one transcription factor and you get an entirely different cell type without the magic of mutations that somehow cause differences in cell types in tissues of organs in organisms that must effectively thermoregulate their cell/body types to survive. How likely is it that a nutrient-dependent alternative splicing and amino acid substitution is involved?
arpotu
1 / 5 (1) Dec 18, 2013
I suspect there will be additional levels of complexity found. After all, DNA is a 2-bit system (four states per rung), and they can have sometimes surprising complexity. A Turing machine is a 1-bit system and, if long enough, supposedly it can simulate consciousness. There are also different sets of DNA running around a cell (nucleic vs mito), which can add to the complexity.
Jaeherys
5 / 5 (3) Dec 18, 2013
JVK:

The first article you posted did not and can not conclude de novo creation of anything as there was NO evidence of it. Your constant use the the phrase "amino acid substitution" separate from genetic mutation is just blatantly wrong. Perhaps more disturbing than your apparent disregard for the evidence going into the definition of the term, "amino acid substitution", is the fact that you don't seem to acknowledge the effects of billions of years of organisms that have lived and died in order to produce what we have today.

Mutation may be deleterious, have no effect, or be beneficial and this is EASILY proven. Not only from natural examples where small changes produce immediate and severe changes in function that can be selected for or against but through human manipulation of genes that change the function, with Tac polymerase being one of the best examples.

You seem quite intelligent yet you purposely bias evidence to fit your hypothesis and this is completely anti-science.
JVK
1 / 5 (1) Dec 18, 2013
Jaeherys: Please try to support your claim for mutation-driven evolution in the context of Dozhanasky's (1964) claim that people who observe morphological variation and report that variation is caused by mutations are akin to bird-watchers and butterfly collectors.

Asserting evidence that amino acid substitutions are due to mutations is theoretical nonsense and that nonsense has been revealed by what is currently known about the conserved molecular mechanisms of ecological adaptation in species from microbes to man.

The double meaning in the genetic code suggests that the millions of years time frame needs adjustment. However, it also attests to the obvious role that a balance of nutrient stress and social stress plays in enabling the conserved molecular mechanisms of ecological adaptations sans mutations.

The fact that you don't like the biological facts does not make them irrelevant -- except in the context of theory, in which the biological facts have never been considered.
Zephir_fan
Dec 18, 2013
This comment has been removed by a moderator.
Whydening Gyre
5 / 5 (1) Dec 18, 2013
Dang, Zeph-skippy. just when I thought you were a complete ass/idiot, you go and post a smart comment....
Zephir_fan
Dec 18, 2013
This comment has been removed by a moderator.
Whydening Gyre
5 / 5 (1) Dec 18, 2013
Dang, Zeph-skippy. just when I thought you were a complete ass/idiot, you go and post a smart comment....


It wasn't intentional. Don't hold it against me. But that JVK Skippy, just won't let that really nice Jaeherys help him. She, or he, was being a lot more patient with him than I would be, and all JVK offered in return was to call her, or him a liar and science fraud. JVK is the one selling the hormonal love potions on the interweb. Jaehery, she, or he didn't appear to be selling anything, only trying to help him.


Apology accepted...:-) And - you are correct in your observation....
Jaeherys
5 / 5 (2) Dec 18, 2013
I am of the male persuasion. And to keep this post from being deleted, codon bias is known to play a role in the regulation of translational efficiency.
JVK
1 / 5 (1) Dec 19, 2013
A report on cell type differentiation in the mouse now links ecological variation to the presence of microRNAs in the circulatory system. In my model, that is how alterations in the microRNA/messenger RNA balance differentiate cell types, individuals, and species based on the biological functions that are stored in the genome.

The circulatory system is not required, nor is anything else except ecological variation, which is why some people will understand how the biological functions that are stored in the genome must be epigenetically effected for cell type differentiation to occur in any species.

A SICB conference held in January was devoted to the topic of ecological epigenetics. That means there are many people who are well-informed about biologically based cause and effect. None of them participate here.

"...DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs..." What causes the DNA changes: ECOLOGICAL VARIATION.
Whydening Gyre
5 / 5 (1) Dec 19, 2013
This link might help illuminate a little.
http://erikandrul...ing-dna/
Zephir_fan
Dec 19, 2013
This comment has been removed by a moderator.
JVK
1 / 5 (1) Dec 19, 2013
Ecological variation is the source of the amino acids that he fails to mention are required for the biosynthesis and de novo creation of genes.
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
[paras combined] Seems to me like this is just more and more evidence of god. I mean, you can only have so many pieces falling together before it becomes a little fishy. We have evolution. Which describes what happened after all the nearly impossible stuff happened. Then we have some sorts of chemistry to describe what happened before any of the hard stuff happened. Spend a few million years watching random bricks fall together, until they make a perfect square. Close your eyes for a few billion years and when you open them, skyscraper! Makes more sense to me that something stopped by and glued us together. lol


Creator of the Universe or bored passerby messing with it's version of Legos at a rest stop. THAT is one heck of a choice there, Sparky! I gave you a five for throwing a full sized monkey wrench into the sandbox. (mixed metaphors, anyone?)

Seriously, Bored Passerby sounds just as probable and Universe Creator Yahweh. I'm starting The Church of the Bored Traveler.
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
scottfos>>> "Zor, it must be nice that no matter what you learn or don't learn it merely reinforces your preconceived notions. almost makes one wonder, why bother learning anything at all? which, of course, explains a lot about so many of your brethren...."

You seem to know a lot about the open mindedness and thinking ability of Zor. Do you know him well? Or are you generalizing from your *own* preconceived confirmation bias?
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
AeroSR71 >>> This isn't evidence of God. That just brings up more questions, such as, which God? After all, humanity's made up thousands of deity's over the years.

That would depend, I would think, on what exactly that 2nd code says.

The best cutting edge cosmological theory of the creation of the universe sounds, to be frank, like the desperate pleadings of a voodoo ghost's High Priest who can't remember all the cons piled on cons. Weasel words? Check. Reader assault w/ jargon? Check. Ad hominem arguments? Check. Appeals to Authority? Check. Sounds religious to me.

(I'm essentially an atheist, but: (1) this current apparent dead end in cosmology, (2) the fact that I think I may have a mathematical proof that there *has* to be a God (but not like any vision of God ever imagined), and (3) a thought that absence of evidence is not evidence of absence, leads me to the conclusion that I have to allow for the possibility of a God (or a Bored Traveler).)

Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
I have a sneaky feeling that a third level of biological instruction will be divined from duon research.


I read a "future documentary" about that. One of Asimov's, I think. A brilliant molecular biologist says to his friend (or someone - years since I read it) that our genetic code is actually a MESSAGE from an alien race that created it 4.3 billion years ago, meant for another race, today. A telegram, if you will.

The friend says, "So?"

The scientist says "There's every reason to believe that the telegram was delivered some time ago."

The implied question of course: What do you do with a telegram once you've read it?
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
>>>zorlont3: "Seems to me like this is just more and more evidence of god. I mean, you can only have so many pieces falling together before it becomes a little fishy. .....[words]..... Makes more sense to me that something stopped by and glued us together. lol"

>>>jxaxmxixn: "Obviously you have not even the most fundamental clue on how chemistry works. You should probably try to learn how atoms are formed, and then how atoms connect together to form all of the simple to complex molecules that make up our planet universe.
The logic you've tried to use here (buildings building themselves, etc...) is NOT how evolution happens! Try reading a science book!

Maybe it's just me, but I thought he was just waxing poetical, and stuff like atoms and molecules can get in the way of that. But I'm new here, so what do I know...
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
JVK: "If this stability, which is probably important to the stability of life itself, results from randomness that somehow enables the thermodynamics of intercellular signalling, stochastic gene expression, and the amino acid substitutions that result in organism-level thermoregulation, which differentiates individuals and species from all other individuals and species via genetically predisposed differences in antigenic properties like those determined by a single amino acid substitution in the human influenza virus, the atheists are right and they could probably prove it."

Serious request and serious question: Could you please restate the above in simpler language. Also why would this prove the atheists right? Thanks.
Old Guy in Stanton
1 / 5 (1) Dec 30, 2013
JinXer >>>>>> "The Christian God is a paradox... their assertion is that he is both Eternal and Omnipotent. Which cannot be. Eternal means that he has always existed and shall always exist, he cannot not exist. Omnipotent means that no action is beyond his abilities. This means that if he so chose, for reasons beyond our understanding, decided to destroy himself he would have the power to do so, and would cease to exist. Well then he's not Eternal. And if he is in fact Eternal then he is not Omnipotent. God is broken."

Good logic. And yet a Universe-creating "God" may in fact exist. In fact, if the probabilities I am thinking of check out, MUST exist. But IT would: (1) be like nothing we have ever imagined, (2) MAY in fact have created us by creating a specific Universe capable of supporting life, but (3) probably does not give a fig about us one way or the other. (4) OTOH he may have a use for us, once we have evolved enough.
JVK
1 / 5 (1) Dec 30, 2013
Thanks for asking. Any experimental evidence that the biophysical constraints on nutrient-dependent pheromone-controlled amino acid substitutions that stabilize all cell types in all organisms arise from randomness instead of ecological variation would refute Dobzhansky's Creationist approach in the widely cited "Nothing in Biology Makes Any Sense Except in the Light of Evolution." Like Darwin, Dobzhansky clearly recognized that 'conditions of life' must be considered before Natural Selection or Sexual Selection.

That's obviously why Dobzhansky (1964) ridiculed anyone who based their opinions on what they could observe. In "Biology, molecular and organismic" he wrote: "...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!

Atheists need experimental evidence of something to support their claims! Otherwise they can't be serious.
JVK
1 / 5 (1) Dec 30, 2013
'Conditions of life' are nutrient-dependent because all organisms must eat. Conditions of life are pheromone-controlled because species specific pheromones control the physiology of reproduction.