Weirder: Dinoflagellate genes all point the same way

_{Denyse O'Leary

May 16, 2021

Evolution, Genomics, Intelligent Design}

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Turns out, they are even less like other eukaryote genomes:

A striking finding was that the genes in the genome tended to be organized in alternating unidirectional blocks. “That’s really, really different to what you see in other organisms,” says Octavio Salazar, a postdoc in Manuel Aranda’s group at KAUST and one of the lead authors of the study. The orientation of genes on a chromosome is usually random. In this case, however, genes were consistently oriented one way and then the other, with the boundaries between blocks showing up clearly in the chromatin interaction data.
This organization is also reflected in the three-dimensional structure of the genome, which the team inferred comprises rod-shaped chromosomes that fold into structural domains at the boundaries where gene blocks converge. Even more intriguingly, this structure appears to be dependent on transcriptional activity. When the researchers treated cells with a chemical that blocks gene transcription, the structural domains disappeared.
This unusual link is consistent with another strange fact about dinoflagellates — they have very few transcription factors in their genome and do not seem to respond to environmental changes by altering gene expression. They may use gene dosage to control expression and adapt to the environment by losing or gaining chromosomes or perhaps via epigenetic structural modifications. The researchers plan to explore all of these questions.
Octavio Salazar, “Coral symbionts have a genome like no other” at KAUST Discovery (April 29, 2021)

The paper is open access.

So how did all this originate randomly, different from what all the other life forms do — and still work?

See also: Dinoflagellate genome structure is unique. So, in other words, these plankton evolved (randomly, so we are told) a highly successful genome that’s entirely different from the type that most life forms have. Well, if you are skeptical of Darwinian claims that it all happened randomly but just once, how about (at least) twice?

Comments

Bob O'H... i apologize, you are right. From my end, it was not necessary. I am just angry when i see all this, and when a Darwinist (not you) calls me 'you stupid creationist'. I apologize. Any rational person (the more a scientist) should see a creation/design behind these things - to believe anything else is like to believe in miracles...to say "we don't know yet / god of the gaps" is not enough. Anyway, when you could look deeper into it, that would be great. I won't check for your update on this in this post, but you can contact me anytime using my contact details at my blog. Just click my UD nickname, it will redirect you to my blog where you will find my contact details/form. Thanks. PS: i doubt you will find any answer. Because, it is like with DNA proofreading & repair subject. I tried to learn how something like that can evolve, i did not find a thing, i even contacted some geneticists in DNA repair research, NOBODY KNOWS (they also said, that i am asking interesting questions) Nobody will ever find an answer how these things ever evolve. Because this can't be evolved. It only can be created/designed by an intelligent agency. The good thing is, that you finally understand my question on gene position.martin_r_{May 19, 2021
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Martin_r - here we were having a perfectly nice conversation, and i was trying to help you understand better. But then you write this:
I understand, that you Darwinists never think about these things, because in your fantasy world, you don’t have to … in your fantasy world works everything flawlessly, no thinking needed, no design needed, just chance and lots of lucky accidents …
You are asking an interesting question, so I would have been prepared to dig deeper (e.g. I did see a comment about how promoters tended to be physically located on the outside of the chromosome), but now I don't see why I should bother.Bob O'H_{May 19, 2021
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BobOH, meanwhile BA77 posted the following: Talbott states, “You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. This is exactly what i meant.... How does the cell know, what is the position of that 'half-inch stretch' within those 24 miles... I understand, that you Darwinists never think about these things, because in your fantasy world, you don't have to ... in your fantasy world works everything flawlessly, no thinking needed, no design needed, just chance and lots of lucky accidents ... PS: BA77 thank you for your post, actually, i am not surprised that nobody knows... this is what i have expected ... but this is pretty serious question if Darwinists want to rule out design...martin_r_{May 18, 2021
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BobOH, no, you still dont get it. I know about stop/start codons and promoters. What i dont understand is, how the cell knows the location/position on chromosomes of particular gene ... chromosomes are pretty huge storage space, how the cell knows where to look ... Let me quote the following “Geneticists use maps to describe the location of a particular gene on a chromosome. One type of map uses the cytogenetic location to describe a gene’s position. “ Does the cell use a map? This is what i meant...martin_r_{May 18, 2021
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Martin_r you asked Bob, "But how (does) the cell know the exact position on (the) chromosome(s) of (any) particular gene?" Contrary to what Bob implied, Bob does not know, nor does anyone else know, exactly how the cell 'knows' the exact position of any particular gene on the chromosome(s). In fact, "cell-intelligence' is, in direct contradiction to a central assumption of Darwinian evolution, "turning our ideas of genetic causation inside out."
Is The Age Of The Gene Finally Over? - January 5, 2019 Excerpt: So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA. That is why today’s molecular biologists are reporting “cognitive resources” in cells; “bio-information intelligence”; “cell intelligence”; “metabolic memory”; and “cell knowledge”—all terms appearing in recent literature.1,2 “Do cells think?” is the title of a 2007 paper in the journal Cellular and Molecular Life Sciences.3 On the other hand the assumed developmental “program” coded in a genotype has never been described. It is such discoveries that are turning our ideas of genetic causation inside out. We have traditionally thought of cell contents as servants to the DNA instructions. But, as the British biologist Denis Noble insists, “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.” … https://uncommondescent.com/genetics/is-the-age-of-the-gene-finally-over/
Stephen Talbott has an excellent article detailing just how amazing it is for the cell to 'know' where a gene is. Talbott states, "You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles.
Genes and Organisms: Improvising the Dance of Life - Stephen L. Talbott - Nov. 10, 2015 Excerpt: The performances of countless cells in your body are redirected and coordinated as part of a global narrative for which no localized controller exists. This redirection and coordination includes a unique choreography of gene expression in each individual cell. Hundreds or thousands of DNA sequences move (or are moved) within vast numbers of cell nuclei, and are subjected to extraordinarily nuanced, locally modulated chemical activity so as to contribute appropriately to bodily requirements that are nowhere codified — least of all in those DNA sequences.,,, DNA in its larger matrix You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene. Except that sometimes one copy differs from the other and one version is not supposed to be expressed, or one version needs to be expressed more than the other, or the product of one needs to be modified relative to the other. So part of the job may be to distinguish one of those half-inch stretches from the other. “Decisions” everywhere, it seems. But no such decisions are made in a vacuum. As it happens, the chromosome does not consist of a naked DNA double helix. Our DNA, rather, is bound up with a massive, intricate, and dynamic protein-RNA-small molecule complex (called chromatin) that is as fully “informative” for the cell as the DNA sequence itself — and, you might say, much more active and directive.,,, the cell, by managing the shifting patterns of the chromatin infrastructure within which DNA is embedded, brings our chromosomes into movement on widely varying scales. These include large looping movements that put particular genes into connection with essential regulatory sequences and with other, related genes (that is, with other one-half inch stretches of our “24 miles of string in a tennis ball”).,,, A gene is not in any case the kind of rigidly defined entity one might hope to calculate with. As a functional unit appropriate to current circumstances, it must be cobbled together by the cell according to the needs of the moment. There is no neatly predefined path to follow once the cell has located the “right” half inch or so of string, or once it has done whatever is necessary to bring that locus into proper relation with other chromosomal loci participating in the same “dance”. One issue has to do with the fact that there are two strands in the DNA double helix and, starting from any particular point, it is possible to transcibe either of two DNA sequences in either of two directions: “forward” along one strand, or “backward” along the other. This yields two completely different products. One of them is very likely not even a protein-coding RNA, and yet it may still play a vital role in gene expression and in cellular processes more generally. And even when the cell would proceed in one particular direction, it must “choose” the exact point in the genetic sequence at which to begin. Different starting points can yield functionally distinct results. “Many studies focusing on single genes have shown that the choice of a specific transcription start site has critical roles during development and cell differentiation, and aberrations in . . . transcription start site use lead to various diseases including cancer, neuropsychiatric disorders, and developmental disorders”.8,,, The (protein) enzyme that transcribes DNA into RNA is RNA polymerase12. The enzyme certainly does not work alone, however, and its task is by no means cut-and-dried. To begin with, its critical interactions with various elements of the pre-initiation complex help determine whether and exactly where transcription will begin, if it is to begin at all. Then, after those “decisions” have been made, RNA polymerase moves along the double helix transcribing the sequence of genetic “letters” into the complementary sequence of an RNA. Throughout this productive journey, which is called elongation, the RNA polymerase still keeps good and necessary company. Certain co-activators modify it during its transit of a genetic locus, and these modifications not only enable transcription elongation to begin, but also provide binding sites for yet other proteins that will cooperate throughout the transcription journey.,,, Finally — and mirroring all the possibilities surrounding initiation of gene transcription — there are the issues relating to its termination. Again, they are far too many to mention here. Transcription may conclude at a more or less canonical terminus, or at an alternative terminus, or it may proceed altogether past the gene locus, even to the point of overlapping what, by usual definitions, would be regarded as a separate gene farther “downstream”. The cell has great flexibility in determining what, on any given occasion, counts as a gene, or transcriptional unit. The last part of the transcribed gene is generally non-protein-coding, but nevertheless contains great significance. Examining this region in a single gene, a research team recently identified “at least 35 distinct regulatory elements” to which other molecules can bind.13 Further regulatory potentials arise from yet more binding sites on the customized “tail” that the cell adds to the RNA immediately upon conclusion of its transcription. Proteins and other molecules that bind to the various regulatory elements of the non-protein-coding portion of the transcript do so in a context-sensitive manner, where cell and tissue type, phase of the cell cycle, developmental stage, location of the RNA within the cell, and environmental factors, both intra- and extra-cellular, may all play a role. These converging influences can change the stability of the RNA, change its localization within the cell, and change the efficiency of its translation into protein, among other possibilities.,,, What is generally considered the post-transcriptional modulation of gene expression actually begins during transcription proper. A prime example has to do with what happens partly as a result of the pauses during elongation. Cells don’t just passively accept the RNAs that emerge from the transcription process, but rather “snip and stitch” them via an elaborate procedure known as RNA splicing. It happens that the cutting out and knitting together of selected pieces typically begins before the RNA is fully transcribed, and the rhythm of pauses during elongation has an important influence upon which pieces form the mature transcript. This splicing operation, which is applied to nearly all human RNAs, is performed by the spliceosome, consisting of a few non-protein-coding RNAs and over 300 cooperating proteins, and is hardly less exacting in its requirements than, say, brain surgery. For the vast majority of human genes the operation can be performed in different ways, yielding distinct proteins (called isoforms) from a single RNA derived from a single DNA sequence. This is called alternative splicing, and it would be hard to find anything in human development, disease etiology, or normal functioning that is not dependent in one way or another on the effectiveness of this liberty the cell takes with its gene products. But RNA splicing is hardly the end of it. Through RNA editing the cell can add, delete, or substitute individual “letters” of the RNA sequence.15 Or, leaving the letters in place, the cell can chemically modify them in any of over one hundred different ways.16 ,,, Eventually, a protein-coding RNA needs to be translated into protein. This happens by means of large molecular complexes called “ribosomes”. Just as with gene transcription, there are many associated factors that must work together to bring about the initiation of translation, many that cooperate with the ribosome during translation, and yet others that play a role in modifying, localizing, or otherwise regulating the newly produced protein. The overall picture of gene expression is one of unsurveyable complexity in the service of remarkably effective living processes.,,, A decisive problem for the classical view of DNA is that “as cells differentiate and respond to stimuli in the human body, over one million different proteins are likely to be produced from less than 25,000 genes”.30 Functionally, in other words, you might say that we have over a million genes.,,, http://www.natureinstitute.org/txt/st/org/comm/ar/2015/genes_29.htm
bornagain77_{May 18, 2021
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Way to totally miss the point, Bob O'H. How did blind and mindless processes cobble all of that together, Bob?ET_{May 18, 2021
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Martin_r - promoters are more than just start/stop codons. They are where the RNA polymerase binds. There are also sequences around them that are specific to the gene, and other transcription factors can bind to them. This provides the basic mechanism - there is a lot more (of course). Are you asking about how genes are regulated?Bob O'H_{May 18, 2021
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BobOH, anybody can answer my question ... Perhaps my question is not clear enough (English is not my first language). Let me clarify: Like i mentioned above, i am aware of start/stop codons, i heard of promoters, but do promoters answer my question ? How the cell knows where to look for the particular gene which needs to be transcribed ? I can imagine, that there are genes that are transcribed all the time... the same genes again and again... but, for example under some stress, a particular gene needs to be transcribed. How the cell knows, where to look for this particular gene DNA sequence ? Start/stop-codon only tells where to start /stop the DNA transcription of the particular gene. But how the cell knows the exact position on chromosome(s) of this particular gene?martin_r_{May 17, 2021
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BobOH, anybody can answer my question ... however, this is not what i have asked. Perhaps my question is not clear enough (English is not my first language). Like i mentioned above, i am aware of start/stop codons, i heard of promoters, but does promoters answer my question ? How the cell knows where to look for the particular gene which needs to be transcribed ? I can imagine, that there are genes that are transcribed all the time... the same genes again and again... but, for example under some stress, a particular gene needs to be transcribe which is usually turned off. How the cell knows, where to look for this particular gene DNA sequence ? Start/stop-codon only tells where to start /stop the DNA transcription of the particular gene. But how the cell knows the exact position in whole DNA molecule of this particular gene?martin_r_{May 17, 2021
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Martin_r - I know you're asking Polistra, but his answer in 1 demonstrates he doesn't understand the subject (in case you're wondering, yes I am a biologist). Anyway, the simple answer to your question is - it's complicated. Genes don't just have start and end codons, they also have promoters - DNA sequences near the start codon that say " a gene starts here", and allow RNA polymerase to bind to them to start transcription. There's more on Wikipedia. Incidentally, I can recommend this book if you want a basic introduction to genetics.Bob O'H_{May 17, 2021
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Polistra, you seem to be well educated. I have an off topic question, perhaps you can help. I am an engineer and don't have a formal education in biology. I was always wondering, the DNA is a very long molecule, how the cell knows, where to look for the right DNA sequence during DNA transcription. I know that there are so called start/end codons, but this is not what i mean. Humans have approx. 20,000 genes, so how the cell know where to look for the particular gene in order to transcript it ... in other words, how the cell finds the proper DNA sequence in this vast storage space ? I hope my question does not sound too silly, but i tried to google it, i could not find any answer. Perhaps you can navigate me ... thank you.martin_r_{May 17, 2021
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" do not seem to respond to environmental changes by altering gene expression. " Note how epigenetics has become the default norm. Lysenko wins.polistra_{May 16, 2021
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