Central Dogma: Missing, and presumed dead

_{Denyse O'Leary

May 29, 2014

Genomics, News}

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Further to “Proteome ‘more complex than previously thought’”, from Science:

“The prevalent view was that information transfer was from genome to transcriptome to proteome. What these efforts show is that it’s a two-way road—proteomics can be used to annotate the genome. The importance is that, using these datasets, we can improve the annotation of the genome and the algorithms that predict transcription and translation,” said Steen. “The genomics field can now hugely benefit from proteomics data.”

Hey, aren’t these the cement shoes of the Central Dogma? Remember when One gene coded for one protein?

See also: Information killed the Central Dogma too

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Comments

Gpuccio:
Still, Piotr has recently stated that no “explicit” procedures are needed. I answered that, in post #108 here: https://uncommondescent.com.....-part-two/ but he has not commented further. I still would like to know where he thinks the procedures are written, explicit or not.
Sorry, Gpuccio, those threads have been buried under a heavy layer of sediments. I'll start commenting here for want of a better place. There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution. DNA sequence doesn't do anything by itself. It contains no program or procedure; it's only data. Life is a complex quasi-periodic process which uses DNA as a memory. The memory is used to store recipies for structural, catalytic, signalling and regulatory molecules -- inherited recipies that have worked in the past. The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible. Proteins are chemicals. They don't think and they don't carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute "step number 8453".Piotr_{June 1, 2014
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RodW: In no way I was implying that you should agree with waht I was saying. I just profited of something that you said, and with which I did agree, to express my ideas. :) I am aware that gene regulation has always been a part of the scenario, but one thing is to reason in terms of promoters and enhancers, or of single transcription factors, another thing is to address the problem of a general informational plan, what I call "the procedures". There has been a gradual shift from a purely mechanistic approach to a more integrated view, but I think that the official scientific position is still very reluctant to admit a very simple truth: the whole differentiation process, and its coordination and control, which allows a same genome to produce hundreds of sophisticated specialized transcriptomes and proteomes, is still completely elusive, not only because we don't know the details (which is not in itself a problem), but because we have really no idea of where the complex procedures that must be there, somewhere, really are. There are those who simply deny that those procedures exist. They seem to think that things just happen for a lucky series of feedbacks, which in some way makes the genome capable of taking the correct path towards each type of cell, of tissue, of organ, of form. But anyone who has even the simplest understanding of how informational systems work can easily realize that such a position is utter folly. When a cell has to activate a definite group of transcription factors, let's say 400, out of the 2000 which are available in its genome, and it has to activate them in definite order and quantity, and regulate them and everything else by complex networks like nuclear RNAs and peptides, alternative splicing, epigenetic processes, post translational modifications, and so on, and those processes are different and specific in each cell type, and in each phase of a single cell type, then it is very easy to understand that what I call "the procedures" is a lot of explicit information, and that it must be coded somewhere. I believe that understanding where and how those procedures are coded should be the absolute priority in this moment. After all, the continuous accumulation of ever growing datasets is making that understanding a little bit easier.gpuccio_{May 31, 2014
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gpuccio
I think you express very well the problem in your last post.....The problem is: “where is it”? The whole subtext of the “central dogma” question is that there has been a general confidence that information was mainly, if not almost exclusively, in the protein coding genes.
Thanks but I don't quite agree with some of what you say. They've known since the 1960s that genes are controlled by non-coding regulatory segments and in the 1970s when they showed that human and chimp proteins are almost identical they concluded that all the differences must come from regulation. Since the 80s many in 'EvoDevo' have asserted the notion that most of animal evolution is due to changes in protein regulation. But its true that new levels of regulation seem to be constantly turning up! Yesterday I read a review article that mentions that protein translation in the cytoplasm can effect transcription in the nucleus. There seem to be a lot of people here who are very interested in this stuff but don't have any 'formal' training. I just don't think its possible to pick it up in bits and pieces. I strongly recommend that those interested buy an advanced text like Molecular Cell Biology by Lodish and read it cover to cover. There are great courses on Youtube like Eric Landers at MIT but I don't think that's advanced enough for people here.RodW_{May 31, 2014
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Are you aware of any theory explaining this accent difference? Could it be that she has a genetic predisposition for languages that I lack? Or could it be that Slavic (particularly Polish) women are better at speaking foreign languages? Thank you.
There are some results showing that women in general (not just Polish ones) have better bilingual skills than men. This may have to do with the fact that the performance of language-related tasks seems to be more strongly lateralised in men and involves more bilateral activation in women (for the same reason brain damage is less likely to affect women's linguistic abilities). There might be an evolutionary explanation of that: if early human communities regularly practised linguistic exogamy (with men taking wives from a different tribe, with a different native tongue, as come societies of the Amazon still do), this could have led to a selective pressure favouring greater plasticity of language-learning skills in women (they had to learn their husbands' languages but not vice versa). But it's only a guess: I'm not aware of any formal studies confirming it. Needless to say, the effect is statistical and doesn't have to be confirmed by each individual case.Piotr_{May 31, 2014
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RodW: I think you express very well the problem in your last post. Central dogma or not, it is obvious that the information for all that will happen (with possible modulations from the environment) is already there, in the zygote (or however in the initial cell for unicellular beings). We could just say that it flows from "where it is" to "where it must go". That is a very general way to describe things, but it should be correct. The problem is: "where is it"? The whole subtext of the "central dogma" question is that there has been a general confidence that information was mainly, if not almost exclusively, in the protein coding genes. But the simple truth is that such a view cannot explain the "procedures": how those genes are used and regulated in so many specific, finely tuned ways, especially (but not exclusively) in metazoa. That important problem has become specially relevant now, when we are beginning to have a general map of transcriptomes and proteomes, not to speak of the whole epigenetic-friendly trend. I hope that the old attitude, of simply pretending that there are no procedures written anywhere, will become sooner or later obviously irrational to all, and not only to us in ID. Still, Piotr has recently stated that no "explicit" procedures are needed. I answered that, in post #108 here: https://uncommondescent.com/intelligent-design/is-functional-information-in-dna-always-conserved-part-two/ but he has not commented further. I still would like to know where he thinks the procedures are written, explicit or not. A very good starting point could be your comment: "In a way you could say that this and other so-called violations of the dogma aren’t really violations, they just reflect the fact that information coded in the DNA is coded in many layers or dimensions." It's exactly those "layers or dimensions" of the coding, which IMO will certainly in many ways include non coding DNA, which can allow some understanding of cell differentiation and function, a topic of some importance, I believe. And a topic of great relevance for the ID debate, given that it is about coded functional information. :)gpuccio_{May 30, 2014
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Dionisio
Now, do those findings you mentioned, relative to the Nature links posted in my comments #3, 4 & 8, conflict with the so called ‘central dogma’ of biology?
That's an interesting question which would probably require several pages of discussion. The Central Dogma states that information flows from DNA to protein, and not in the reverse direction. None of the supposed examples of violations of the dogma I've seen have included RNA editing, but it seems to me it should be included. On the other hand, the enzyme that edits RNA is coded for in the DNA, and the place and time of its expression is controlled by DNA. In a way you could say that this and other so-called violations of the dogma aren't really violations, they just reflect the fact that information coded in the DNA is coded in many layers or dimensions. As an aside I'll say that I was a Biochemistry major for 4 years and took grad classes and was in grad school for 6+ years and in all that time I heard the phrase 'Central Dogma' mentioned once- in an undergrad class. Most scientists don't concern themselves with it. You wouldn't even call it a theory..its a sort of generalization. I think I recall hearing that the word 'dogma' was meant a bit tongue-in-cheek ( mistake earlier - my friend worked on Shaker not ADAR. ADAR is the enzyme)RodW_{May 30, 2014
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#24 RodW
I think the point of the Nature paper from 3 years ago was that they used data from the human genome along with new info on proteins that were directly sequenced and found an unexpectedly large number of genes edited in humans. I can look up stuff if you have more questions!!
Thank you for the explanation, which seems to answer the questions in my comments 3, 4, 8. Now, do those findings you mentioned, relative to the Nature links posted in my comments #3, 4 & 8, conflict with the so called 'central dogma' of biology?Dionisio_{May 30, 2014
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#21 BA77 Thank you for sharing that interesting information. I'm sure many talented folks who write in this blog can understand that report much better. But I definitely enjoy anything I can get out of it. Your comments usually have interesting links and quotes. Thank you for the effort you make to compile that information and share it here. Many interesting reports -like the one you have shared with me- will keep appearing in the scientific media at an increasing rate, as the research technology turns more precise and efficient. These are exciting times for scientists and for the rest of us who follow closely the results of their research work. Still much remains unknown. For example, in this case the report says: “However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level.” That’s why we should look forward, with much anticipation, to the news coming out of the labs, which will shed more light on the amazing biological systems we are so eager to understand. Currently I'm busy -sweating and struggling- while trying to understand the mind-boggling mechanisms associated with the precise timing of the centrosome segregation for the effectiveness of the spindle apparatus operating on the intrinsic asymmetric mitosis during the initial stages of human embryonic development. I take frequent breaks to rest. Sometimes during those breaks, I check to see what's going on in this blog. There are many interesting areas in biology that I would like to read about, but can't do it, because time is very limited and goes by very fast, I'm a slow reader, my reading comprehension is rather low, and my IQ score is similar to my age ;-) That's why I enjoy reading the free abstracts of some papers that are behind paywalls. Those compacted summaries are sufficient to excite my imagination. ;-) Rev. 22:21Dionisio_{May 30, 2014
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Piotr, Thank you for sharing that detailed information on the story behind that part of the English language. I could not describe that well even my first language (Spanish) ;-) Now, let me take advantage of this opportunity to ask you a language related question about spoken accents. My wife and I have very different accents in English, even though we both came together to the US and have a comparable knowledge of the language (well, perhaps she knows it slightly better than I do). Could it be that the noticeable accent difference has to do with our first languages being so different too? There are sounds in Polish languages that I still can't pronounce correctly, and probably never will. However, my wife speaks Spanish without accent. She can pronounce all Spanish sounds like any person in Madrid, where we lived before moving to the US. She even claims that Spanish is much easier to learn than other languages she knows or is familiar with, including French, German and English. Are you aware of any theory explaining this accent difference? Could it be that she has a genetic predisposition for languages that I lack? Or could it be that Slavic (particularly Polish) women are better at speaking foreign languages? Thank you.Dionisio_{May 30, 2014
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Dionisio I think ( not sure) that editing was first discovered in protists and later fruit flies. The guy I knew worked on the ADAR gene in drosophila which is edited. I'm not sure when the first human ( or vertebrate) edited gene was discovered. I think the point of the Nature paper from 3 years ago was that they used data from the human genome along with new info on proteins that were directly sequenced and found an unexpectedly large number of genes edited in humans. I can look up stuff if you have more questions!!RodW_{May 30, 2014
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Dionisio:
However, these days most potential readers wouldn’t have noticed the difference between “its” and “it’s”
Actually, "these days" are not so different from "days of yore". The possessive pronoun its became acceptable in literary English about 1640, well after Shakespeare's death. Until that time, the possessive form of it had been his (of Old English origin, and Shakespeare's regular choice), or the periphrastic genitive of it. Its was an innovation, formed on the analogy of "Saxon genitives" like William's. The spelling it's was very common until about 1800, when the variant without the apostrophe began to prevail and came to be regarded as standard.Piotr_{May 30, 2014
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Piotr, An "Edit" button would be a nice feature. I could use it many times ;-) However, these days most potential readers wouldn't have noticed the difference between "its" and "it's". As an English language specialist you know that better than I do. Przyjemnego 'weekendu' !Dionisio_{May 30, 2014
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Dionisio, this may interest you: Does a Kitchen Sponge Have a Function? - May 30, 2014 Excerpt: A recent paper in Nature shows that there is a small, non-coding RNA, transcribed from DNA, that acts as a "protein sponge" to soak up the excess. It can then "squeeze" the extra proteins back out for work, when conditions are favorable.,,, This is no ordinary sponge. It has a "well-defined" structure that is "well-tuned" to sequester proteins.,,, the molecule works in a "cooperative, well-defined and regulated manner," as opposed to the "random fashion",,, The authors were surprised to see such finely tuned design in a simple molecule whose only role is to act as a sponge. Each binding induces a conformational change, so that proteins are bound and released in sequence.,,, http://www.evolutionnews.org/2014/05/does_a_kitchen086171.htmlbornagain77_{May 30, 2014
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Dionisio, I noticed the superfluous apostrophe the moment I was clicking on "Post". Unfortunately, there's no "Edit" button.Piotr_{May 30, 2014
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Piotr, malutka poprawka:
Is it junk news? It may have some space-filling and structural functions, but it’s sequence doesn’t matter.

Is it junk news? It may have some space-filling and structural functions, but its sequence doesn’t matter.
Dionisio_{May 30, 2014
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Is it junk news? It may have some space-filling and structural functions, but it's sequence doesn't matter.Piotr_{May 30, 2014
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You forget Acartia, this is a "News" post so there is no requirement for the post content or title to match the linked article. Such minor details would just get in the waywd400_{May 30, 2014
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So, what dogma is being busted her? Rather than using the genes to identify the proteins, they are using the proteins to identify the genes.Acartia_bogart_{May 30, 2014
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# 12 RodW
RNA editing has been known about for about 15-18 years. I knew someone who worked on it in 1999
That's interesting. Thank you for sharing that information. Back in that year you mentioned (1999) I was busy working overtime on a software development project for engineering design applications on PC. My wife was busy working on software development for business applications on large IBM mainframe systems. Back then the only editing I knew was to write or maintain programs written in C language. My wife edited her programs written in COBOL, DB2, CICS, etc. My children knew more biology than I did back then. Today they are both doctors in medicine, so they still know more biology than I do (well, many people out there know more biology than I do). Ok, enough digression, let's go back to the subject. If, as you stated, RNA editing has been known for so long, then why did a respected peer-reviewed publication like Nature dared to publish 3 years ago the two articles I mentioned in my comments # 3 & 4, which clearly give the impression they were kind of surprised? Does that make sense? Also the Nature article linked in my comment # 8 seems to present a similar dilemma, even though it was written just over a year ago. Can you explain this apparent contradiction? Thanks again.Dionisio_{May 30, 2014
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RodW- Just because we know of RNA editing doesn't mean unguided evolution didit.Joe_{May 30, 2014
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edit (third-person singular simple present edits, present participle editing, simple past and past participle edited) To change a text, or a document.Mung_{May 29, 2014
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Dionisio RNA editing has been known about for about 15-18 years. I knew someone who worked on it in 1999RodW_{May 29, 2014
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I thought this thread was going to be about the fast & convergent evolving to avoid parasitic fly crickets in Hawaii chirp chirp. Talk about Dogma Busting:) And the fly's have cricket ears. What is THAT all about?ppolish_{May 29, 2014
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BA77 Thank you for the information.Dionisio_{May 29, 2014
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Dionisio this may help a bit Demise of the Gene - September 19, 2012 Excerpt: Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order framework around which individual transcripts coalesce, creating a poly-functional entity that assumes different forms under different cellular states, guided by differential utilization of regulatory DNA. (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.) http://www.evolutionnews.org/2012/09/demise_of_the_g064371.html Gene activity and transcript patterns visualized for the first time in thousands of single cells - Oct 06, 2013 Excerpt: The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells. Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells.,,, The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.,,, http://phys.org/news/2013-10-gene-transcript-patterns-visualized-thousands.html Here’s That New Paper Showing the Genetic Regulation Hierarchy - Cornelius Hunter - September 2012 Excerpt: a massive study of the interactions between transcription factors and DNA. The study found that the action of transcription factors falls into three distinct, hierarchical, categories. There are interactions that specify the basic cell type (muscle, skin, nerve, and so forth). Then there are interactions that specify the cell’s sub-identity (the particular type of muscle cell, for example). And finally there are interactions that specify the cell’s response to the current environmental challenges. http://darwins-god.blogspot.com/2012/09/heres-that-new-paper-showing-genetic.htmlbornagain77_{May 29, 2014
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Molecular biology: The ends justify the means A genomic analysis of yeast reveals that individual genes produce a rich complexity of RNA molecules with differing start and end sequences. The variation in these transcripts reflects the diversity of gene-regulation mechanisms. http://www.nature.com/nature/journal/v497/n7447/full/nature12098.html
This was published over a year ago - has it been confirmed or disproved since then? Does it relate to the subject of this thread?Dionisio_{May 29, 2014
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Yes, I knew what your point was immediately and agree with you.Mung_{May 29, 2014
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I'm not sure if you're joking, Mung. But I was going to point out that the "information flow" in the central dogma doesn't refer to what humans know about biology. Making that mistake is about the only way you could imagine this study relates to the central dogma, as far as I can tell.wd400_{May 29, 2014
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wd400:
The roll continues. Unless you want to explain what on earth this finding has to do with the central dogma?
Well, you see, we can now annotate genomic information with information from proteomics, and this shows that information transfer isn't strictly one way, from genome to transcriptome to proteome, as maintained by the Central Dogma. It's simple, really. =P I can't believe I have to explain this to you. ;) To me the even bigger News is, this information that now goes the other way along this "two-way road," where does that information come from?Mung_{May 29, 2014
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Evidence of altered RNA stirs debate Sceptics question find that upends biology's 'central dogma'. http://www.nature.com/news/2011/110525/full/473432a.html
This was published about 3 years ago - has it been confirmed or disproved since then?Dionisio_{May 29, 2014
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