The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.
Curiosity drives us to find answers along our unique life paths. For Adam B. Dorfman, that path began with an MBA at the University of Toronto and with several years in the capital markets before he began to look into a career in science.
Adam then studied the frontiers of different fields, with each new revelation revealing that many new sciences were about to change civilization. After founding Conceptual Revolutions, where he features leading scientists in these emerging fields of study, he wrote the book, Conceptual Revolutions in Science.
Let's see how this works. The article published on Feb. 7, 2016 looks interesting. It's title is Epigenetic News, How Long Noncoding RNA Can Regulate Colon Cancer. The "paradigm shifting" news is "How junk DNA actually regulates colon cancer."
That's pretty interesting, isn't it? The article was written by Nicholas Morano (@nickmorano) who is working on a Ph.D. in biochemistry at Albert Einstein College of Medicine, Yeshiva University, in New York (USA). Here's the first two paragraphs,
Long Noncoding RNA – A lot of us may remember learning in high school biology that only a very small fraction of the genome actually contains genes; the rest of it is nonfunctioning “junk” DNA. As is common in science, the last 10 years of biological research have proved this hypothesis to be very wrong. The traditional central dogma of biology taught that DNA is a template for making RNA and that RNA is a template for making protein.Regular Sandwalk readers will cringe at the number of errors and misconceptions packed into such a short space. I'll list them for the benefit of readers coming from the outside,
However, researchers have recently discovered that a large part of what we once considered to be junk, actually codes for many different types of RNA molecules that don’t make protein and play important roles in regulating cellular functions. One such class of RNA molecules is known as long noncoding RNA (lncRNA). These are large molecules of RNA that exhibit enzyme–like functions in the cell.
- Only a small fraction of the human genome contains genes but no knowledgeable scientist every claimed that all the rest was junk DNA.
- The last 10 years of biological research has confirmed the conclusions of the previous 30 years that about 90% of our genome is junk DNA.
- The actual Central Dogma of Molecular Biology is NOT "DNA makes RNA makes protein." [The Central Dogma of Molecular Biology]
- Researchers have NOT recently discovered that a large part of our genome contains genes for functional RNA molecules. They've known for 50 years that there are genes for functional RNAs. Beginning about 25 years ago, they discovered many members of new classes of genes for regulatory RNAs. These genes account for less than 1% of the human genome and that number is not likely to get much larger.
- A small number of lncRNAs are known to have functions but they are not "enzyme-like."
Long Noncoding RNA – A lot of us may remember learning in high school biology that only a very small fraction of the genome actually contains genes;There! That's better.the rest of it is nonfunctioning “junk” DNA.As is common in science,the last 10 years of biological research have proved this hypothesis to be very wrong.The traditional central dogma of biology taught that DNA is a template for making RNA and that RNA is a template for making protein.
However, researchers have recently discovered thata largepart of what we once considered to be junk, actually codes for many different types of RNA molecules that don’t make protein and play important roles in regulating cellular functions. One such class of RNA molecules is known as long noncoding RNA (lncRNA).These are large molecules of RNA that exhibit enzyme–like functions in the cell.
115 comments :
if most of the genome is junk then how is that we see a correlation between the complexity and the amount of suppose junk?:
http://www.ncbi.nlm.nih.gov/pubmed/23759593
we also know that plants with a big genome grow very slowly. so maybe this junk actually functional after all?.
onion test.
Paradigm Shaft.
The idea of the "Paradigm Shift" is due for a paradigm shift
"if most of the genome is junk then how is that we see a correlation between the complexity and the amount of suppose junk?"
We don't.
"we also know that plants with a big genome grow very slowly. so maybe this junk actually functional after all?."
Citation needed.
Dorfman: These are large molecules of RNA that exhibit enzyme–like functions in the cell.
Well, that's a newly discovered species of stupid.
Eh, barrel. Shooting. Fish.
Creationist says "we also know that plants with a big genome grow very slowly. so maybe this junk actually functional after all?"
Utricularia gibba has the smallest genome of any flowering plant. Please explain why plants in the Utricularia–Genlisea clade vary widely in genome size, with reference to the functional necessity of wildly varying genome sizes.
I'll wait.
here is one example:
http://www.telegraph.co.uk/news/science/science-news/8196572/Worlds-largest-genome-belongs-to-slow-growing-mountain-flower.html
So you're ignoring our questions, and changing the subject over to a claim that enormous, enormous genomes are all functional.
Say, has it ever occurred to you that the bigger a genome is, and the larger is the fraction of functional base pairs, the more mutations there must be?
What do you think about mutations? Mostly beneficial? Mostly neutral? Or, like other creationists, do you say all mutations are "Catastrophic!!"
Well, pal, the bigger a genome is, and the larger is the fraction of the genome that's functional, the more "CATASTROPHES!" you have every time a seed grows into a flower. How could any of these species live?
i think that most of the mutations are neutral. again- how do you explain that there is a correlation between complexity and the size of the junk?
Google "dog's ass plot". That should help.
Like NickM said: Onion test.
Though in dcsccc's case, it may well be that an onion is more complex than he is, at least in terms of cognitive processing.
You're not troubled that Paris japonica has a genome 50 times larger than humans (and by your logic 50 times more complex)? Also, the actual scientist who made this discovery said: "Genome size does not necessarily relate to the complexity of an organism.". Someday you may realise that real scientists are far cleverer than creationists who cherry pick from press releases.
Circling the wagons eh, Larry?
IncRNA's are comin' to bite you like a junkyard dog, haha!!!
Here I was thinkin' Larry's acting days were over.
Oh well, Gitty up pardner!
My father would say about guys like Dorfman: "He takes himself much too seriously."
@dcscccc
"http://www.telegraph.co.uk/news/science/science-news/8196572/Worlds-largest-genome-belongs-to-slow-growing-mountain-flower.html"
So you extract a general principle from a single case. You know you can't do that, right?
Also, that flower is now supposed, according to the rule you extracted from your ass, to be simultaneously the most complex organism in existence and the slowest growing one.
It is neither. You are wrong on all counts.
"we also know that plants with a big genome grow very slowly. so maybe this junk actually functional after all?."
The fact that it generally takes longer to copy a larger stack of paper doesn't mean every page contains useful or functional information. Even if you write random noise and nonsense on 100 pages, it still takes the time it takes to copy those 100 pages as it would if it contained Shakespeare.
Steve continues to play the annoying yappy chihuahua while offering nothing substantive to the conversation.
Adam then studied the frontiers of different fields, with each new revelation revealing that many new sciences were about to change civilization.
Perhaps this sort of stuff helps bring in investment from other MBAs.
Larry, you seem to be in the minority in regards to this junk DNA debate. I've talked to some old friends of mine, one who did his PhD in genetics at Cornell (now a professor at U. Virginia) and one who did his PhD in evolutionary biology at U. Rochester (now in industry) and both have said they don't believe that most DNA is junk...
I'm not a biologist so I don't really know one way or another, but I do have a question:
Why not just remove pieces (obviously not all, at one) of DNA that we think are junk from an organism and see if it messes up the organism or not? Wouldn't that give some indication as to what's junk and what isn't? Has this been done?
There are some fine natural experiments in that direction. Fugu would be one of them.
You should ask your friends how they deal with the evidence that most of the human genome is junk. Direct them to Larry's posts on the subject, to start.
They basically chalked it up to older math models that don't hold up to newer experimental evidence. They acknowledge there is SOME junk DNA, but not the majority.
Since most biologists don't agree with Larry, I find it hard to believe that all of them, or even most of them, are unaware of the supposed evidence for junk DNA. I think they're more impressed with experimental evidence.
I doubt your limited sample of friends is a good index of what "most biologists" think. Again, how do your friends deal with that evidence. If it's just sneering at "older math models" and touting "newer experimental evidence" (ENCODE?) I don't think much of their claims.
In my experience, it would seem true that "most" biologists think that there's little to no junk DNA. However, the very same biologists talk in the exact mistaken terms that Larry keeps pointing out. They seem unaware of the evidence for junk. Nothing about "outdated" mathematical models. It's more ignorance. Seems also like many scientists make a quick judgement out of simplified and cartoonist versions of how the junk DNA was thought about. Seems also like many quickly turn to it for a career, still on the cartoonist version. Lots of pose with little substance, unfortunately. Scholarship is gone (if there ever was any).
John, Larry himself has said he talked to biologists at a conference and that he was in the minority.
Most of the junk DNA I've seen is based on models like the c value stuff, not actual experimentation. The results from ENCODE seem to be very well accepted. The blurb about them weakening their argument doesn't mean that they are declaring most of their transcriptions to be spurious, they are acknowledging it is possible.
Again, why not just start removing portions of genomes of organisms that supposedly have a lot of junk?
Most of the junk DNA I've seen is based on models like the c value stuff, not actual experimentation.
What are you talking about? The c-value paradox comes from experimentation. I suspect that you do not know what that means.
The results from ENCODE seem to be very well accepted. The blurb about them weakening their argument doesn't mean that they are declaring most of their transcriptions to be spurious, they are acknowledging it is possible.
Did you or did you not notice that in order to declare that 80% of the DNA was functional they used their very own definition for "functional"? Check it out yourself. My argument here is this: if you're going to say that o DNA is junk, then you better use your terms properly. Otherwise you're engaged in equivocation.
Again, why not just start removing portions of genomes of organisms that supposedly have a lot of junk?
This has been done in mice, and the mice seem to be all right. I don't have the citation now. There's also the observations that you think are merely theoretical, like some pretty simple organisms harbouring ridiculously huge amounts of DNA, etc, etc. There' also some complex ones with small genomes almost devoid of anything that's not genes.
The whole picture is that junk DNA exists, and that the amount in eukaryotes varies enormously. That we humans harbour quite a good amount of it.
What biologists did Larry talk to? Were they evolutionary biologists with an interest in molecular evolution? Anyone else would be irrelevant.
"The c value stuff" isn't a model; it's an observation. You seem to prize experimentation above other sorts of observation. Why? What do you think the ENCODE results show, and why are they an argument against most of the genome being junk?
Once again, fugu is a natural experiment of the sort you propose. How is it that fugu do just fine with an eighth of the human genome?
"The c-value paradox comes from experimentation. I suspect that you do not know what that means."
It looks at genome sizes which is based on measurement, but then makes the assumption that the large genome size (when comparing members of two similar, but different species) is mostly junk DNA. It hasn't been established experimentally.
It's quite simple. Remove the DNA that you think is junk and show that the organism is unaffected.
"What biologists did Larry talk to?"
I don't know. That's from his blog a while ago. He wrote it. I didn't. Ask him. Larry? What conference was it?
>You seem to prize experimentation above other sorts of observation. Why?
The observation is the genome size, right? From the observation, the genome is concluded to be junk, meaning you can remove 90% of it and the organism would be just fine. That's one hell of a conclusion to draw. The "junk" part isn't the observation, it's the conclusion. ENCODE has given some evidence to suggest that this assumption is wrong. Even with their weakened statement, they acknowledge that transcription *may* not necessarily mean function, but they don't conclude that most of the transcriptions are spurious.
>Once again, fugu is a natural experiment of the sort you propose. How is it that fugu do just fine with an eighth of the human genome?
Every time someone looks for function in DNA, they find it. Pretty much every investigation into finding some kind of function has turned up positive.
I've seen a small handful of studies were a few genes have been removed and the organism appeared to be fine, but that's it.
Most proponents of non-junk-DNA acknowledge there will be some genes that are junk.
It looks at genome sizes which is based on measurement, but then makes the assumption that the large genome size (when comparing members of two similar, but different species) is mostly junk DNA. It hasn't been established experimentally.
Bzzzt! Sorry, wrong. Thanks for playing, creotard.
The c-value paradox is an observation that requires an explanation. Junk DNA provides an explanation. No one who denies the existence of DNA has been able to provide another explanation. Including you.
I'm a creationist now? You realize most biologists do not believe that most DNA is junk, right? Are most of them creationists now?
>Junk DNA provides an explanation.
Sure, but it's an explanation that hasn't been put to the test. The test is simple: remove it and see what happens. It's really that simple. What are you afraid of?
It very much is an assumption that most of the DNA is *removable* junk based on a comparison of genome sizes.
Again, even Larry has admitted this: most biologists don't hold that view.
The hypothesis of junk DNA has been tested a couple of ways. There was the mouse knock-out experiment with suspected junk removed; mice were fine. There was an observational experiment on college students; they sequenced part of their own genomes and found that they varied in the presence or absence of patches of DNA thought to be junk -- and no problems were associated with the absences. Both fugu (a fish) and the bladderwort Utricularia gibba lack nearly all hypothesized junk DNA seen in their relatives, and they do fine. On the other hand, not only do onions have a lot more DNA than humans, but the amount vary within a species (and often at the diploid level) in the amount of DNA they have, and the differences don't seem to have a phenotypic effect.
Then there are the calculations you dismiss, about the expected effects of the observed mutation rate in humans and other species, if all their DNA were functional.
The evidence for junk DNA is strong, and all the stronger because most biologists who go to the trouble to argue against it demonstrate failure to understand what the term junk DNA means, the history of the terminology, and/or the evidence for it.
Damn you, ENCODE Project, for destroying another "evidence" for evolution... The laughable concept of "Junk DNA"..
Absence of transitional forms and signs of gradualism in the fossils, no documented case of mutations generating new relevant information, orphan genes, junk DNA destroyed, human phylogenetic tree dismantled by many studies...
Evolution is rushing to its dead-end, where it will face the same fate as spontaneous generation..
I'm a creationist now? You realize most biologists do not believe that most DNA is junk, right?
No, I don't know that. Care to support this assertion with some evidence? (Prediction: You're just blowing hot air.)
Sure, but it's an explanation that hasn't been put to the test. The test is simple: remove it and see what happens. It's really that simple. What are you afraid of?
"Remove it"? Remove what, exactly? Let's provide a hypothetical example. Suppose there is a section of DNA, 99% of which is junk, but 1% of which comprises a regulatory sequence for a vital function. If we remove this section of DNAm the organism dies. So what do you think we have demonstrated? That the entire section of DNA is functional? Is that what you think? Maybe. It's possible that you're that stupid.
>No, I don't know that. Care to support this assertion with some evidence? (Prediction: You're just blowing hot air.)
Larry Moran said it himself. Photosynthesis said the same thing. From the few that I've talked to, even biology students here at Georgia Tech, said the same thing.
>"Remove it"? Remove what, exactly?
Remove sections of DNA that you think are junk and see what happens. That would address your 99% vs 1% issue. Identify some regions, specifically, and remove them. If you can't do that, then you're conflating "unknown function" with no function.
It's been done:
http://www.nature.com/news/2004/041018/full/news041018-7.html
This is stupid. Evolution and junk DNA are disjoint.
That just establishes that junk DNA exists. I've read that article, years ago. You're late to the game.
How much DNA do they actually remove in that study? Not very much.
Since you're big on ENCODE's qualifer, let me quote you the qualifier from the author of this study:
"Knowles cautions that the study doesn't prove that non-coding DNA has no function. "Those mice were alive, that's what we know about them," she says. "We don't know if they have abnormalities that we don't test for."
So, there you go. This doesn't establish your case at all. Creotard.
And it also turns out that this DNA likely does have some function:
https://www.newscientist.com/article/dn22009-mouse-junk-dna-vital-for-gene-regulation/
You seem to be ignoring the entire fugu point. Again, it's a natural experiment of exactly the sort you inexplicably demand.
"Evolution is rushing to its dead-end, where it will face the same fate as spontaneous generation.."
Spontaneous generation has been successfully recycled. They call it origin of life studies now.
I'm not ignoring the fugu thing. The argument is that because the fugu fish has 1/8 of a genome size as humans, that humans must have a lot of junk DNA (90%).
Since it hasn't been tested if this DNA can be removed without affecting the organism, this could represent an unknown function. It can't be concluded to have "no function."
I’m not sure how to evaluate this paper but it seems quite relevant.
“New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation”
http://rstb.royalsocietypublishing.org/content/370/1678/20140332
“The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages….”
“… it has now become clear that de novo origin of protein-coding genes from non-coding DNA is a consistent feature of eukaryotic genomes, having been discovered in organisms as diverse as yeast, plants, flies, mammals, primates and even in recent human evolution.”
This seems to indicate the non-coding regions are an important source of novel genes. It seems ‘junk’ might not be the best description if that is the case.
read this post from about 2 weeks ago on this site, http://sandwalk.blogspot.ca/2016/01/origin-of-de-novo-genes-in-humans.html
The DNA you think isn't junk is mostly dead retrotransposons. We know how dead retrotransposons look,they look like transposons with deleterious mutations in them. Something like >40% of the human genome is made of dead retroelemnts. It doesn't do anything.
It is mutating at a neutral rate(aka not conserved), which means it's not maintained by natural selection.
It is spuriously transcribed at a level commensurate with noisy binding, which is an unavoidable consequence of how transcription factors bind to DNA.
It's what we see in other species too. We know the mehanism that generates it (transposons randomly inserting themselves in the genome and then getting deactivated by mutations).
Additional DNA is pseudogenes (another few %). We know how pseudogenes look, they look like protein coding genes with inactivating mutations in them(premature stop codons, missing exons, degraded initiaion of transcrition regions etc.)
Then there's retroviral elements, dead ALUs, LINEs, SINEs, countless scrambled and dead (because of mutations in their sequence)reverse tanscriptases. They are not conserved. They show varying levels of degradation (by mutation) commensurate with a historical process of noisy generation, accumulation and deactivation.
It's junk. Most molecular biologists are wrong, and sadly (and concerning) unqualified to speak about it. Get over it.
Still noone hs discovered an ORfan with a known function. What is being discovered is that some junk regions are being transcribed and translated, as would be exepected if the junk is mutating randomly at a neutral rate and therefore coincidently happen to look like an initiation of transcrition-region and so on. ORFans aren't evidence against junk.
I wish the people who argue against junk would bother to understand the basics of transcription and the underlying principles first(how trsndcrition happens, how DNA-binding proteins work, how they find their target sequence etc). It is remarkable how many of these purported arguments against junk DNA that can be rebutted simply by knowing something about the basics.
@Wallace
Name 1 function discovered by ENCODE.
@Jai Dayal
No, they aren't. Genetic load and sequence conservation are arguments for junk that also rely on evolution. They are not totally diconnected subjects.
@txpiper
Nobody believes spontaneous generation happens. Everybody knows it takes more than a mere dilution of organic molecules for living cells to form. So you're just straightforwardly wrong.
It helps a lot when you know what the word mean. Spontaneous generation is not synonymous with abiogenesis. SG refers to a specific hypothesis, not the entire field.
Creationism made you ignorant, but you can change that if you want to.
But Mikkel it has all been intelligently designed so if it is transcribed it must have a function therefore it is all functional and we are intelligently designed. It's so simple.
How much DNA do they actually remove in that study? Not very much.
Wrong. The sections removed were 1511 and 845 kb in length. According to this, the average length of a eukaryotic gene is 1.2 kb. So that means they removed the equivalent of almost 2,000 genes. Do you think if someone removed 2,000 of your genes it would have no effect? OK, maybe that's a bad example. If 2,000 genes were removed from the genome of a normally functioning person (as opposed to a neurodegenerated creationist like yourself), do you think it would have no effect? LOL!
"Knowles cautions that the study doesn't prove that non-coding DNA has no function. "Those mice were alive, that's what we know about them," she says. "We don't know if they have abnormalities that we don't test for."
So, there you go. This doesn't establish your case at all. Creotard.
Oh. So, IOW, you were lying. When junk DNA is removed from a genome and the organism continues to function normally, you don't accept this as evidence for junk DNA, You just shift the goalposts and say "OK, it may look normal. But is it really normal?" Typical. Your ignorance is matched only by your dishonesty.
This seems to indicate the non-coding regions are an important source of novel genes. It seems ‘junk’ might not be the best description if that is the case.
Where else would you expect novel genes to come from, than the vast majority of genetic and gene-like material available, i.e., the ~10% of our genome that isn't "junk," and the ~90% that is?
The fact that you've been able to scavenge something useful from a rubbish heap doesn't mean it isn't a rubbish heap. It also doesn't mean a random pile of junk hanging around has some higher (or in fact any) "purpose." It's just there, it's available, and every so often a bit of it randomly mutates into something useful, harmful, or (mostly) just plain neutral.
Where else would you expect novel genes to come from, than the vast majority of genetic and gene-like material available, i.e., the ~10% of our genome that isn't "junk," and the ~90% that is?
Well, they could be poofed into existence out of nothing by an omnipotent "Intelligent Designer". It's very interesting that that isn't the way it happens. I wonder what ID proponents make of this odd state of affairs.
>Wrong. The sections removed were 1511 and 845 kb in length. According to this, the average length of a eukaryotic gene is 1.2 kb. So that means they removed the equivalent of almost 2,000 genes. Do you think if someone removed 2,000 of your genes it would have no effect?
Actually, they state it right in the article that they moved at most 1% of the genome for the paper. That's stated in the article and interview directly.
>you don't accept this as evidence for junk DNA,
You have very very bad reading comprehension. Almost at a juvenile level. Nobody argues that "there is absolutely no junk DNA at all". The argument is how much DNA is junk. Larry believes that 90% of the DNA is junk. Most biologists, according to Larry even, do not accept this view and believe the amount of junk DNA is much lower.
That's the argument we're having. I've already said this earlier in this very thread that some junk DNA exists. You clearly need to work on your reading comprehension.
I'm not ignoring the fugu thing. The argument is that because the fugu fish has 1/8 of a genome size as humans, that humans must have a lot of junk DNA (90%).
Since it hasn't been tested if this DNA can be removed without affecting the organism, this could represent an unknown function. It can't be concluded to have "no function."
So what are these "unknown functions"? And why are they so well hidden that no one has been able to detect them?
The corollary of the fugu fish is that some species of salamanders have genomes that are over 40x the size of humans'. So I guess that means there are a lot of "hidden functions" in the salamander genome that we don't have. What are these? It should be easy to find at least some of the thousands of proteins, biochemical pathways, etc that salamanders possess that are absent in us. Where are they? Why haven't any researchers identified these?
>No, they aren't. Genetic load and sequence conservation are arguments for junk that also rely on evolution. They are not totally diconnected subjects.
Genetic load makes sense in the context of neutral mutations. Mutations can be neutral without there being junk DNA. For DNA that produces protein products, most mutations will not drastically change the protein structure.
Simple test: find the 90% of the genome that you think is junk and remove it and see what happens.
In Jai Dayal's defense, I think his/her post above was attempting to say that evolutionary theory is not dependent on the presence or absence of junk DNA. Which is exactly correct.
Simple test: find the 90% of the genome that you think is junk and remove it and see what happens.
Right. All you have to do is identify every single part of the genome that has a function. Piece of cake, anyone could do it.
Are you really this stupid?
"Genetic load makes sense in the context of neutral mutations. Mutations can be neutral without there being junk DNA. For DNA that produces protein products, most mutations will not drastically change the protein structure."
Try deleting an exon and then rationalize it as being neutral.
"In Jai Dayal's defense, I think his/her post above was attempting to say that evolutionary theory is not dependent on the presence or absence of junk DNA. Which is exactly correct."
That's true. But beyond the theoretical understanding of how the mechanism takes place, there is also the observations of the actual genomic sequences and structures in different organisms. These are in turn explained by evolution. If there's no such thing as junk, evolution as we know it can't explain what we see.
Are you really this stupid?
I realize that rhetorical questions are questions you ask to make a point. You don't really expect an answer.
However, this particular one has an obvious answer.
Again, even Larry has admitted this: most biologists don't hold that view.
Let's be very clear about what I actually meant.
Yes, I believe it's true that most biologists are skeptical about junk DNA. Most of them think that a large fraction of our genome must be there for a reason. Their views are reinforced by an incompetent popular press that publishes misleading and incorrect information about junk DNA and by publications in the scientific literature written by scientists who haven't done their homework.
This doesn't mean what you think it means. Most biologists are not experts on the subject of genomes and evolution and they haven't studied the question or read the literature. There's nothing wrong with that. None of us can keep up with everything in biology.
When you want to know the answer to a particular question you ask the experts, not the amateurs. The vast majority of knowledgeable biologists who have studied genomes and evolution have reached the conclusion that most of our genome is junk.
I'm confident that I'm reporting the opinions of the experts, not the amateurs.
> Actually, they state it right in the article that they moved at most 1% of the genome for the paper. That's stated in the article and interview directly.
That's the same thing you twit. Whether you express it as a percentage or not, it's still the equivalent of about 2000 genes worth of DNA.
Larry, you admitted it yourself in a previous blog post that most biologists you've talked to do not agree with you on the extent of junk DNA. I think before you start calling people stupid, you should ask yourself why you're largely considered a kook in the great community.
>So what are these "unknown functions"? And why are they so well hidden that no one has been able to detect them?
Let's be clear. You're the one assigning these pieces of DNA with a function. The NULL function is very much a member of the set of functions F = {f0, f1, f2, ... fn}. You're the one claiming it's known that most DNA is assigned to one of these f's, namely the NULL f.
The truth is, though, any time someone looks for function on some level, they find it. Take the mouse example. They found over 40% of the mouse DNA serves some epigenetic role. That's a lost less junk DNA than 90%.
>In Jai Dayal's defense, I think his/her post above was attempting to say that evolutionary theory is not dependent on the presence or absence of junk DNA. Which is exactly correct.
Yes, that's exactly my point. Of course, the knee-jerkers here think everyone who disagrees with 90% junk DNA is a creationist.
John Mattick was right: the reason these non-scientist die hards have such a problem with DNA not being junk is because they feel ENCODE invalidates a large part of their argument against creationists. There are lots of good arguments against creationism. Junk DNA isn't one of them.
>That's the same thing you twit. Whether you express it as a percentage or not, it's still the equivalent of about 2000 genes worth of DNA.
Correct. What I'm clarifying for you is that 1% junk != 90% junk.
So I suppose you think that they just so happened to randomly pick out the 1% that actually was junk while missing out all the other stuff which you think is functional but have yet to provide evidence for?
> why you're largely considered a kook in the great community
Really? who can you cite to represent "the great community"?
> Let's be clear. You're the one assigning these pieces of DNA with a function. The NULL function is very much a member of the set of functions F = {f0, f1, f2, ... fn}. You're the one claiming it's known that most DNA is assigned to one of these f's, namely the NULL f.
You saw it here... This is where the creationist begins to lay the foundation for the claim that not having a function is actually a function after all.
> 40% of the mouse DNA serves some epigenetic role
You obviously don't know what epigenetics is. How can DNA serve an epigenetic role? By definition, epigenetic markers sit on top of DNA.
> That's a lost less junk DNA than 90%
The 90% claim applies only to humans. Some species have a lot of junk DNA, some have a little. I don't know what the number is for mice.
> 90% junk DNA is a creationist
Not everybody, but we do get loads of creationists stopping by and this is a common trope.
> John Mattick
(Probably a closet creationist - his talking points sound eerily familiar)
> There are lots of good arguments against creationism. Junk DNA isn't one of them.
I don't think junk DNA is a good argument against creationism. But creationists seem to think that it's supposed non-existence is a good argument for creationism. Our only interest is to defend the science against ideologues.
Correct. What I'm clarifying for you is that 1% junk != 90% junk.
Wrong again (for a refreshing change of pace). What it does demonstrate is that, when a large sequence of DNA that has been identified as junk is deleted, is has no observable effect. This suggests that when knowledgeable researchers identify sections of DNA as junk, they actually know what they are doing and they are not just making an argument from ignorance, as you insinuate.
Can you explain why a salamander's genome is 40x larger than ours, if most of that excess genetic material is not junk? You seem to have avoided that question.
@Jai Dayal:
Evolution has done the experiment. Stuff that's important to survival and reproduction is conserved (e.g., HOX genes). Stuff that's not important comes and goes at a rate consistent with the "molecular clock," the general rate of mutation. (In other words it is not conserved - selected for - nor selected against, in which case it would go away more rapidly.)
Pretty simple, really.
"Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky
Remember that.
Jai Dayal,
I repeat, are you or are you not aware that in order to declare no junk ENCODE used their very own definition for function?
Then you said that most of those who look for a function in "junk" find it. This is a bit misleading. Those who "look for a function" already suspect one, and you get to read about the successful ones. There's little to no reporting of negative results there.
Yes. Every time I look for socks in my sock drawer, I find socks. So I guess if I looked for a pair of my socks orbiting somewhere in the Crab Nebula, I'd find them there, too. Is that what you think Jai Dayal?
lutesuite, how do you know a pair of your socks aren't in the crap nebula? Have you looked?
http://i.imgur.com/msDNHpW.png
:D
>Really? who can you cite to represent "the great community"?
Typo. Meant "greater" community.
>This is where the creationist begins to lay the foundation for the claim that not having a function is actually a function after all.
I don't know or care about what creationists do. Creationists eat dinner. Are all who eat dinner creationists?
What I'm claiming is that you proclaim to know what junk DNA is for. The empty set is a subset of all sets, so technically I am correct no matter how you try to spin it.
>(Probably a closet creationist - his talking points sound eerily familiar)
I used him as an example because I saw Larry's post on him a few months ago calling him a closet creationist. He's not. You can ask him.
You can ask pretty much any biologist who studies evolution and who has heard of Larry Moran. He's pretty much unanimously considered a kook.
>Right. All you have to do is identify every single part of the genome that has a function. Piece of cake, anyone could do it.
People *are* doing it, actually: https://www.newscientist.com/article/dn22009-mouse-junk-dna-vital-for-gene-regulation/
Like I said: when they look for some level of function, they find it.
I checked out " https://www.newscientist.com/article/dn22009-mouse-junk-dna-vital-for-gene-regulation/"
The second sentence shows that the writer doesn't know what she's writing about: "Non-coding, or junk, mouse DNA contains vast amounts of information vital to gene function – and those regulatory functions take up much more space on the genome than the all-important coding segments."
Junk DNA does not equal non-coding DNA. Important non-coding DNA includes regulatory sequences, telomeres, centromeres, etc. Those important non-coding DNA sequences are not junk DNA. They never have been included in the definition of junk DNA used by anybody who understands about the topic. It has been known for a long time that more DNA performs other functions than codes for proteins, in humans and mice.
Therefore, this article is not a reliable source, though it may point to interesting information elsewhere.
The estimation that 11% of mouse DNA may regulate gene expression seems high, and that is news. It's not death to the junk DNA concept. In fact, this article suggests 80% or more of mouse DNA is junk. (2% protein coding, 11% regulatory, and some left for the kinds of DNA not considered in this article.)
You can ask pretty much any biologist who studies evolution and who has heard of Larry Moran. He's pretty much unanimously considered a kook.
Really? What is your sample? I haven't discussed Larry's kookitude with anyone else, but I can offer at least a few counterexamples. Joe Felsenstein. Me. Dan Graur.
More importantly, since science is not a popularity contest, what are the arguments of those who think he's a kook? You don't seem to be presenting any.
You can ask pretty much any biologist who studies evolution and who has heard of Larry Moran. He's pretty much unanimously considered a kook.
Oh, really? Care to name names? How about Dan Graur? T. Ryan Gregory? Jerry Coyne? Joe Felsenstein? If they consider Larry to be a kook, they're awfully circumspect about it. True, those just happen to be biologists with significant on-line presences. I'm not an insider in the field, so don't regularly converse with working biologists in order to know their opinion on this. But it's a bit strange that the majority of evolutionary biologists of whom I am aware know of Larry and do not think of him as a kook. An odd coincidence, don't you think? Or maybe you are thinking of scientists like Micheal Behe and Douglas Axe. Are those the people whose opinions you value?
People *are* doing it, actually: https://www.newscientist.com/article/dn22009-mouse-junk-dna-vital-for-gene-regulation/
I think you might have inadvertently posted the wrong link. That article does not even remotely identify every single functional element of the genome. Or maybe your reading comprehension is just too rudimentary to realize this.
Like I said: when they look for some level of function, they find it.
So tell me: For what percentage of, say, transposable elements has a function been found? All of it, you think?
DGA
Thanks. I overlooked that. The paper I linked to supports the conclusion there.
Mikkel
I think the ‘table 1’ in the paper I linked to includes genes with known function.
ESRG, or QQS, for example.
judmark-
One man’s junk is another man’s treasure.
Maybe ‘junk’ is a good term because there is certainly treasure in novel genes.
The paper I linked to says this-
“The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages.”
The paper is dated 31 August 2015.
Why do you suppose it took so long for the scientists to consider what is apparently quite obvious to you?
Sorry if that seems a bit forward, but it seems you make light of decades of research like the scientists are a bunch of dolts.
Explain yourself.
@ Jai Dayal,
Some direct positive evidence for junk DNA in yeast (which has a much more densely organized genome to begin) is the "artificial" chromosome that left out ~14% of the native chromosome sequence. Including things like the transposons...
The next big test is when this sort of effort is applied to, say the fruitfly or C. elegans.
http://www.nature.com/news/first-synthetic-yeast-chromosome-revealed-1.14941
Sorry if that seems a bit forward, but it seems you make light of decades of research like the scientists are a bunch of dolts.
Explain yourself.
I think you misunderstand judmarc's question. Given that de novo genes occur, whence would they originate if not junk DNA? What other possibility is there?
It is remarkable how many of these purported arguments against junk DNA that can be rebutted simply by knowing something about the basics.
And it is remarkable how little the basics are applied, even in the primary literature.
Mikkel Rumraket Rasmussen,
“It helps a lot when you know what the word mean. Spontaneous generation is not synonymous with abiogenesis.”
Yes, it does help to know things like that. Merriam-Webster defines spontaneous generation as “a now discredited notion that living organisms spontaneously originate directly from nonliving matter —called also abiogenesis”.
"Where else would you expect novel genes to come from...?"
"Over the years, scientists have proposed several mechanisms by which new genes are generated. These include gene duplication, transposable element protein domestication, lateral gene transfer, gene fusion, gene fission, and de novo origination."
http://www.nature.com/scitable/topicpage/Origins-of-New-Genes-and-Pseudogenes-835
txpiper,
Have you understood what those words mean? In the space of time that nonfunctional DNA hangs around before it is fortuitously co-opted for a function, what happens to it? And what proportion of this DNA is actually known to have been recruited to functionality?
Well done Txpiper, you can use a dictionary, the problem is you've missed the context, obviously embracing the only answer you find acceptable. What your dictionary is trying to explain is Generatio spontanea.
"The truth is, though, any time someone looks for function on some level, they find it."
No, they don't. Simple false and pulled directly out of your ass. One of the problems here is you don't actually understand what these researchers do, what their assays show. The fact that molecule A binds to B doesn't mean A or B is functional. Most assays simply discover some kind of interaction. There's a veritable chasm between having discovered a bona fide organismal function and a mere accidental chemical interaction.
"Genetic load makes sense in the context of neutral mutations. Mutations can be neutral without there being junk DNA. For DNA that produces protein products, most mutations will not drastically change the protein structure."
There's more to mutations than mutations in protein-coding regions, as you should well know. You seem to think the only thing that matters are mutations in coding regions.
"Simple test: find the 90% of the genome that you think is junk and remove it and see what happens."
Yeah, it's so simple. You have absolutely zero idea how difficult work this is. Another thing to ponder for you regarding the mouse megabase deletion experiment. If Most DNA is functional, how come removing 2 megabases of DNA still yield viable mice? Your silly retort that they only removed 1% of the total DNA is irrelevant, since this seems to require they by sheer luck happened to remove the only junk-DNA in the mouse genome. You realize the functional pieces are spread out over the genome right? It would be exceptionally improbably to happen to cut out a large piece of DNA without there (if most DNA was functional) happening to be important functional regions in it.
Your response now was to move the goalposts and try to insinuate that there are somehow "hidden" functions in the DNA.
If you're going to respond like this every time, what use would it even be to perform your suggested experiment and remove the 90% junk? You'd still be able to claim there could be mysterious hidden functions in the removed DNA that just haven't come to express itself under the right circumstances.
Instead of this useless blather about removing 90% DNA, how about you specify more direct what DNA you think certainly is functional and how much there is, instead of these vague suggestions?
"People *are* doing it, actually: https://www.newscientist.com/article/dn22009-mouse-junk-dna-vital-for-gene-regulation/
Like I said: when they look for some level of function, they find it. "
Oh my god you ignorant dimwit, that article makes the mistake of thinking non-coding = claimed as junk. Dude, get a fucking education before you come here and blather. Enhancers and promoters were known about like.. 40 years ago, at least? Nobody who ever studied this stuff ever thought that DNA coded for proteins and nothing else, but the write of that article is remarkably confused and uneducated. What a total travesty.
"Mikkel Rumraket Rasmussen,
“It helps a lot when you know what the word mean. Spontaneous generation is not synonymous with abiogenesis.”
Yes, it does help to know things like that. Merriam-Webster defines spontaneous generation as “a now discredited notion that living organisms spontaneously originate directly from nonliving matter —called also abiogenesis”."
Yes, this confirms exactly what I said. Spontaneous generation refers to the specific and falsified hypothesis that life will spontaneously assemble merely from a mix of the individual building blocks of which cells are made. Nobody believes this. There are no credible, contemporaneous models of abiogenesis that postulate this is how life began. They all involve, at the very least, some kind of cyclic event to concetrate products and enchance certain reactions. None of this was part of the original spontaneous generation hypothesis.
Here's encyclopedia:http://www.britannica.com/science/abiogenesis
Quote: "Abiogenesis,
the idea that life arose from nonlife more than 3.5 billion years ago on Earth. Abiogenesis proposes that the first life-forms generated were very simple and through a gradual process became increasingly complex. Biogenesis, in which life is derived from the reproduction of other life, was presumably preceded by abiogenesis, which became impossible once Earth’s atmosphere assumed its present composition.
Although many equate abiogenesis with the archaic theory of spontaneous generation, the two ideas are quite different. According to the latter, complex life (e.g., a maggot or mouse) was thought to arise spontaneously and continually from nonliving matter. While the hypothetical process of spontaneous generation was disproved as early as the 17th century and decisively rejected in the 19th century, abiogenesis has been neither proved nor disproved."
So now you will never again have to mistakenly conflate the two terms. You have learned something new, rejoice!
Chris B,
"Have you understood what those words mean?"
Yes. They represent wishfully thought answers to questions about how in the sam hill can accidents result in functional genes.
Except the part where it's proven facts. Denialist.
Ed,
“the problem is you've missed the context”
No, the problem is not context. It is lack of cognizance that materialism has made its way back to an already “obsolete body of thought”.
===
Mikkel Rumraket Rasmussen
“Yes, this confirms exactly what I said.”
You bet.
-
“Spontaneous generation refers to the specific and falsified hypothesis that life will spontaneously assemble merely from a mix of the individual building blocks of which cells are made. Nobody believes this. There are no credible, contemporaneous models of abiogenesis that postulate this is how life began. They all involve, at the very least, some kind of cyclic event to concetrate products and enchance certain reactions. None of this was part of the original spontaneous generation hypothesis.”
You have to love subtlety and nuance. I think you’ll be safe if you put the contemporary models in the falsified hypothesis file.
"You have to love subtlety and nuance."
Your preference for simplicity reflects your understanding. Simple mind, simple answers, have fun with that.
"I think you’ll be safe if you put the contemporary models in the falsified hypothesis file."
You're basically saying that because mountains don't form spontaneously in a dilution of dissolved minerals, that means all theories of mountain formation are falsified.
It doesn't follow.
Mice do fine without 'junk DNA'
http://www.nature.com/news/2004/041018/full/news041018-7.html
"And it also turns out that this DNA likely does have some function:"
Some of it. Did you read the article, or just like the title?
No, the problem is not context. It is lack of cognizance that materialism has made its way back to an already “obsolete body of thought”.
I guess that would make it unlike Young Earth Creationism, then, which I'm sure has lots of graduate students and published papers and conferences - they just happen to be somewhere no one ever sees them.
Yes. They represent wishfully thought answers to questions about how in the sam hill can accidents result in functional genes.
So much wishful thinking, I'm sure very unlike the mindset it takes to disbelieve virtually all of science for the past 150 years in favor of a set of 1600 year old stories.
Tell you what, turn on your TV, tune to the antenna, and make sure you have no antenna connected. See those dots crawling around, a/k/a "snow"? That's the cosmic microwave background radiation remaining from the Big Bang ~13.7 billion years ago. Right there on your TV. Look at it.
I suppose that ol' joker God just poofed that stuff into existence 6000 years ago but decided to make it *look* really old, right?
Your preference for simplicity reflects your understanding. Simple mind, simple answers..."
Mikkel, the problems with any or all of the OOL proposals are anything but simple. They are all about numerous essentially zero-probability events occurring. If any of them were simple, they could be demonstrated.
What events are those and how do you calculate the probability of them happening? I notice you say they affect ALL OOL proposals. Then please bring me these supposed vast probabilistic issues that affect all models for the origin of life and tell me how you get the numbers you do.
Show me.
Technically only somewhere around 1-10% of the oldfashioned TV-"snow" is due to theCMBR, the rest is other forms of radio noise :P
"how do you calculate the probability of them happening?"
The same way I'd calculate the probability of you being able to jump over a hundred foot wall, or run a 19 second mile. It can't happen.
txpiper said: "Mikkel, the problems with any or all of the OOL proposals are anything but simple. They are all about numerous essentially zero-probability events occurring. If any of them were simple, they could be demonstrated."
Does that include the zero-probability of life being created by the fictional characters yahoo-yeshoo-holy-spook? If not, maybe you can demonstrate that they did it?
The whole truth,
“Does that include the zero-probability of life being created by the fictional characters yahoo-yeshoo-holy-spook?”
That’s a popular tactic. And it may relieve you in a cog-diss moment, but it does not make sappy materialist ideas any more viable, realistic or probable. You could well default to panspermia before you accept the pulp that passes for science in regards to origins.
-
“If not, maybe you can demonstrate that they did it?”
If you’re looking for authentication, plenty of information has been on the books for centuries. Isaac Newton spent decades studying the book of Daniel and the Revelation because he was comfortable with the concept of foreknowledge. You like evolutionary predictions, and he liked the profoundness of prophecy.
Unfortunately, people tend to only believe things that they like, and you don’t really like ‘the whole truth’. That’s why you are here in a support group to keep you away from it.
"The human genome contains roughly 20,000 protein-coding genes, yet the number of proteins in human cells is thought to be more like 100,000. Researchers from three institutions in North America have now shown that at least some of the diversity of proteins’ functions in the cell may be due to the widely diverging roles of protein isoforms—structurally similar variants produced as a result of slight differences during the translation of a single gene......“From the perspective of all the protein interactions within a cell, related isoforms behave more like distinct proteins than minor variants of one another,” study coauthor Tong Hao of Dana-Farber said in the statement."
http://www.the-scientist.com/?articles.view/articleNo/45316/title/Same-Gene--Different-Functions/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=26197263&_hsenc=p2ANqtz-8xJBZPL75vxUozMpmf__ByaUjWk1Cwpi0RvGMV4qOMkoGVxnyK9cywqgJpBK3WrEItW9aSeaqSOl_6fead1EJ8k2MKOQ&_hsmi=26197264
In so many other words, this means that there is a network of regulatory mechanisms behind proteins and protein variants.
"The same way I'd calculate the probability of you being able to jump over a hundred foot wall, or run a 19 second mile. It can't happen."
You're simply regurgitating the claim I asked you to show the truth of, through deductive mathematical logic. You claim the probability is 0. Prove it.
You did have math in school right? Show your work.
"Unfortunately, people tend to only believe things that they like, and you don’t really like ‘the whole truth’. That’s why you are here in a support group to keep you away from it."
We didn't ask for insights in how your psyche works, but since you seem to be saying you only believe in things you like (oh wait, you're somehow the superior exception to your general trend?) maybe you should stop being irrationally biased and look at the facts?
I'm interested in some of the predictions Newton made based on his study of the Bible, and whether they have been fulfilled. Are there any similar to the Einstein's materialist prediction of the existence of gravitational waves?
txpiper brainlessly regurgitates:
"Over the years, scientists have proposed several mechanisms by which new genes are generated. These include gene duplication, transposable element protein domestication, lateral gene transfer, gene fusion, gene fission, and de novo origination."
Very good!. Now, can you point out which of those is the equivalent of "magically poofed into existence out of nothing by an invisible wizard"?
txpiper continues his insipid drooling, thusly:
In so many other words, this means that there is a network of regulatory mechanisms behind proteins and protein variants.
Hey, great! You're finally starting to pick up some of the stuff that was obvious to most everyone else on this blog. Still waiting to see you clarify how this demonstrates that an invisible wizard created it all out of nothing 6000 years ago.
“You claim the probability is 0. Prove it….You did have math in school right? Show your work.”
But Mikkel, you’re going about this backwards. As with the amazing authority of mutations, origin of life absurdities are something that you believe. Did you ask for mathematical proof when you adopted these beliefs? Let’s say that someone is trying to convince you that Elvis is running a boutique on Saturn. You should be asking for reasons to accept such a notion before you make it a bedrock part of your worldview. If you don’t, no matter how stupid the idea is, it stands as fact till someone can disprove it.
===
lutesuite,
“I'm interested in some of the predictions Newton made based on his study of the Bible, and whether they have been fulfilled.”
I doubt that, but his commentaries are online.
I doubt that, but his commentaries are online.
Really? No answer? Not even a link? So were just bullshitting, as usual. At least you're consistent.
I can link you to his commentaries, but you don't have a frame of reference for what he was writing about.
https://www.blueletterbible.org/commentaries/newton_isaac/
As to predictions based on his studies, Newton was writing some 300 years ago. But he recognized that the meanings of the forecasts were deliberately obscure when they were recorded, and still puzzling to him. Nevertheless, he realized that the centerpiece of the apocalyptic scenario would be the regathering of the Jews, and the reformation of national Israel. He wrote:
“…since the commandment to return and to build Jerusalem, precedes the Messiah the Prince 49 years; it may perhaps come forth not from the Jews themselves, but from some other kingdom friendly to them, and precede their return from captivity, and give occasion to it; and lastly, that this rebuilding of Jerusalem and the waste places of Judah is predicted in Micah 7:11, Amos 9:11, 14, Ezek. 36:33, 35, 36, 38, Isa. 54:3, 11, 12; 55:12, 61:4; 65:18, 21, 22, and Tobit 14:5 and that the return from captivity and coming of the Messiah and his kingdom are described in Daniel 7, Rev. 19, Acts 1, Matt. 24, Joel 3, Ezek. 36, 37, Isa. 60, 62, 63, 65 and 66 and many other places of scripture. The manner I know not. Let time be the Interpreter.” Chapter 10
We, having considerably more clarity now, recognize that the “some other kingdom friendly to them” were nations and people reacting to the war 2 holocaust. At this point, we are trying to identify and observe as the pieces and players fall into place. It is obviously a very broad and complex landscape, but we have a mandate to watch. So we watch.
OK I'm a little late for this, but there is another typo ...
"[junk DNA] actually codes for many different types of RNA molecules"
No! DNA (and RNA) codes for protein sequences.
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