The Gene Is Having an Identity Crisis 257
gollum123 writes "New large-scale studies of DNA are causing a rethinking of the very nature of genes. A typical gene is no longer conceived of as a single chunk of DNA encoding a single protein. It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but rather RNA. The familiar double helix of DNA no longer has a monopoly on heredity: other molecules clinging to DNA can produce striking differences between two organisms with the same genes — and those molecules can be inherited along with DNA. Scientists have been working on exploring the 98% of the genome not identified as the protein-coding region. One of the biggest of these projects is an effort called the Encyclopedia of DNA Elements, or 'Encode.' And its analysis of only 1% of the genome reveals the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be and do. The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. Different kinds of cells appear to produce different transcripts from the same gene. And it gets even weirder. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel."
Comment removed (Score:3, Interesting)
Surprise, surprise! (Score:1, Interesting)
This from the people who claimed that most of the DNA in our cells was just junk. I wonder why they were so bloody arrogant? Couldn't they just have acknowledged that they had no clue?
Re:Memory RNA (Score:4, Interesting)
I'd venture a guess that it's not correct (simply not enough evidence supporting it, but that has not yet been ruled out either [nih.gov].
The bottom line is that we do not yet fully understand memory, in much the same way that we do not fully understand synapse formation in the brain. We should just wait and see before jumping to any conclusions (and maybe write a grant proposal or two along the way).
...or not (Score:4, Interesting)
Re:Memory RNA (Score:2, Interesting)
More interesting still was his machine that took cell detritus and 'instant elsewhere'd' it to an adjoining chamber. The idea being to flush the junk from cells and cause a fountain of rejuvenation. FTA, it might be one day feasible to ride a cell of bad or junk RNA.
How many genes does it take to invent a light bulb (Score:5, Interesting)
I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.
It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.
Poetry is both the most compact and the most subtle form of written expression.
This latest finding suggests to me that something similar applies to our genetic heritage.
-S
An analog? (Score:3, Interesting)
Does anyone else see the resemblence between DNA and crufted up old legacy software? Concepts about how heredity works get turned on their head once the mechanisms are examined in detail. I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.
Re:How many genes does it take to invent a light b (Score:4, Interesting)
I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.
It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.
Uh, I remember when they discovered that too, and I don't recall any scientists "freaking out" because the low number of genes implied we had low "complexity". Instead, I remember them being very excited, because they already knew there are far more than 30,000 proteins generated from our DNA, meaning that the 1:1 gene:protein mapping theory had to be wrong, and the mechanism was far more complicated than previously thought.
This sounds to me like a continuation of the line of inquiry opened by that discovery years ago, where now they're gaining a better idea of how the genes really code for proteins. With the extremely interesting aspect that some of this is controlled by things not part of the DNA itself, yet which can still be inherited.
To (ab)use your analogy, if the human body is a work of literature then proteins are the words, and genes are characters. The number of words hasn't changed, it's just that before we thought the language was like Chinese, where a single character mapped to a single word. Now we realize it's more like English, where the interactions between characters create different words. Oh and now we've discovered that there's also punctuation like apostrophes and hyphens which can significantly alter the meaning of the resulting words.
Re:An analog? (Score:3, Interesting)
I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.
Already [icnet.uk] discovered [wikipedia.org].
-Ted
Re:How many genes does it take to invent a light b (Score:2, Interesting)
Re:How is any of this new? (Score:4, Interesting)
Some of it is new, but none of it is surprising to anyone who has been paying attention for, I dunno, the past decade.
It's been clear since the mid-90's when we learned that there were only 44k "coding" genes but at least ten times that many proteins that more was going on than simple templating.
Things like methylation of double-stranded DNA have been known to be important in oncogenesis for at least ten years. miRNAs have been considered important for five years or more. Other conserved non-coding regions have been known for almost as long or longer.
This story is going to be like that "green" story that reports breathlessly every year or so that some company has instituted green policies because they save money! Just like Interface did fifteen years ago, and hundreds of others have done since.
The interesting thing is that these persistently "new" stories give us a measure of how slowly what can fairly be called "general knowledge" changes. Based on evidence from the "green" story we can expect to be hearing the AMAZING NEWS that there's more to genes than template coding until at least 2020.
Following the details as we learn them is fascinating. Being told that an uncontroversial fact we've known for a decade or more is "news" is very, very irritating.
Re:Memory RNA (Score:3, Interesting)
Stimulus-response patterns that are inherited, not learned. Some might exclude mere reflexes (patterns where the stimulus creates the response before/without brain activity) but I'm not sure that modifies the definition in a helpful way.
It's really an interesting question. Seeming complex behavior patterns are clearly not learned, but present in each generation - where do they come from? This would seem to be software, not hardware, but where and how it it stored/passed on?
Re:Memory RNA (Score:4, Interesting)
Memory is an entirely different system, in which patterns simulating previous stimuli are stored and available to be replayed or compared against. Calling the effect of instinct "ancestral memory" or "genetic memory" is at best a poetic interpretation, at worst a logical flaw similar to Lamarkian Evolution [wikipedia.org] wherein giraffes have long necks because their ancestors stretched out trying to graze from tall shrubs, then trees, rather than the Darwinian idea that giraffes have long necks because short necked giraffes did not live to reproduce as well as long necked ones.
Re:Memory RNA (Score:2, Interesting)
Re:Memory RNA (Score:4, Interesting)
Raising both a two year old and a seven month old, there appears to be precious little instinct. Maybe dancing to music.
Re:Memory RNA (Score:1, Interesting)
That is, your body does not contain any device that can write memory information to RNA strands.
Hmm ... a good argument, but I don't think it's quite complete. For example - there are enzymes in cells that break RNA down into its component nucleotides. Some scraps of RNA (eg, with a G' cap) take longer to be broken down than others. Perhaps some enzymes, themselves regulated by other processes, can preferentially break down particular RNA sequences? Then information can be stored, not in the RNA sequences themselves, but in the relative concentrations of particular preexisting sequences.
Of course, this is pure speculation - I don't know of any research that actually implicates RNA as a mental memory mechanism.
Re:Memory RNA (Score:4, Interesting)
>>The way I understand it is that a large part of evolutionary theory ASSUMES that memory can't be inherited.
Maybe not memory per se, but certain phenomena have demonstrated Lamarckian style inheritance.
Mm, DNA can be methylated, which modifies its behavior. A fat pregnant mother will methylate the genes in the fetus, resulting in a kid much more genetically prone to being fat. Experiments with dutch prisoners of war during WWII showed that even when raised under similar conditions, kids from mothers who ate more when they were pregnant were much more prone to obesity.
There's also effects like http://en.wikipedia.org/wiki/Genomic_imprinting [wikipedia.org] which modify an offspring's genome on the fly between generation and generation.
Gotta Quote Firesign Theatre.... (Score:2, Interesting)