Uncommon Descent Serving The Intelligent Design Community

Origins of Genomic ‘Dark Matter’ Discoverd–Once Again, ID Predictions are Spot On

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

This just in from Phys.Org.

Pugh added that he and Venters were stunned to find 160,000 of these “initiation machines,” because humans only have about 30,000 genes. “This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery.” . . .

The remaining 150,000 initiation machines—those Pugh and Venters did not find right at genes—remained somewhat mysterious.
These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists,” Pugh said. “In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins.” [Yeah, that’s right—you called it “junk DNA” and said it was proof contradicting design.] . . . . .

Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes. . . . . . .

These non-coding RNAs have been called the ‘dark matter’ of the genome because, just like the dark matter of the universe, they are massive in terms of coverage—making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there,” Pugh said. “Now at least we know that they are real, and not just ‘noise’ or ‘junk.’ Of course, the next step is to answer the question, ‘what, in fact, do they do?'”[Really?!! “Dark Matter?” You called it “junk-DNA”; it’s only now, now that you’ve been proven wrong on a grand scale that you’ve decided to call it “dark matter.”][P.S. This is what liberals do: when wrong, change the words; e.g., “global warming” = “climate change”, or, “pro-abortion” = “pro-choice”. You see, it all depends on what the meaning of “is” is.]

So, let’s see: 150,000 “initiation machines” (Wow, are there “machines” in the cell?) in the Non-Coding, and 10,000 in the coding portion. I wonder which is more important???? And what has ID been predicting since the late 1990’s? That the Non-Coding portion of the genome is where the bau-plan (blueprint, more or less) of the animal is to be found, and that proteins are but the building blocks (kind of forming the “parts list” of life’s manufacture); i.e., that ‘genes-coding’ portions of the genome are of less importance to life than the ‘non-coding’ portions. Here, it is 15:1 in favor of the Non-Coding—and in full agreement with ID predictions.

And, guess what, finally we get to put to rest the ‘junk-DNA’ argument. How do I know? Because it’s now called “dark matter.”

Comments
#48
So if your mother chose to have an abortion lets say at the beginning of the second trimester – she would not have aborted “you?”
If the entity that existed at that time had no thoughts, feelings, emotions, etc - in other words the qualities that define "me" - than I would say that "I" didn't exist yet. Obviously, an abortion would prevent me from coming into being, but so would have the abortion of my great great grandfather.
But if she waited until end of the third trimester she would have aborted “you?” So the mere separation of three months and the ability to “think” is what constitutes personhood? In “order” for you to get to think….”you” had to go through the second trimester. A human being has to grow and develop – true….but it doesn’t all of a sudden pass a certain moment and “Poof” “you” exist.
Without a brain capable of thoughts, in what sense does a "person" exist? But as I said, when that occurs is very difficult to say, and it isn't a suddent event.
If “you” failed to go through the first two trimesters, “you” would never be able to “think” and you would never be born and you would never be writing on this blog. Thanks to your mother and father….on one certain “day” they helped to create the VERY BEGINNING of “YOUR” life.
Yes, the first two trimesters were necessary for my existence, and so was my great great grandfather meeting my great great grandmother.goodusername
September 18, 2013
September
09
Sep
18
18
2013
09:42 PM
9
09
42
PM
PDT
Liddle, Not only do different religions not agree when a fetus becomes a person, even courts cannot decide. In fact, there is no way to decide that a fetus bcomes a person when the heart appears, or there is a fully formed brain or when such and such development threshold is reached. So the only logical position is the one VJ Torley supports; that the moment the sperm enters the eggs and the first division takes place, that's when a person starts. Any other position is just shaving puzzle pieces in frustration. Hey, but whatever happened to the OP? Can we talk about GDM (genomic dark matter) or is this too much of a 'dark' subject??? Liddle: "Secondly, like Bruce, I do not think it is a given that a conceptus/embryo/foetus is “a baby”. I agree with Bruce that the idea of ensoulment at conception is a religious idea, and not even all religions agree as to when a foetus becomes a person."Steve
September 18, 2013
September
09
Sep
18
18
2013
09:29 PM
9
09
29
PM
PDT
#47 So if your mother chose to have an abortion lets say at the beginning of the second trimester - she would not have aborted "you?" But if she waited until end of the third trimester she would have aborted "you?" So the mere separation of three months and the ability to "think" is what constitutes personhood? In "order" for you to get to think...."you" had to go through the second trimester. A human being has to grow and develop - true....but it doesn't all of a sudden pass a certain moment and "Poof" "you" exist. If "you" failed to go through the first two trimesters, "you" would never be able to "think" and you would never be born and you would never be writing on this blog. Thanks to your mother and father....on one certain "day" they helped to create the VERY BEGINNING of "YOUR" life.Johnnymack
September 18, 2013
September
09
Sep
18
18
2013
09:14 PM
9
09
14
PM
PDT
#45 If I were asked that question, I would answer that I began to exist when I had a brain developed sufficiently enough that I could "think". It's hard to say when that was, but probably early in the 3rd trimester. Before that time I would say that that there was no personhood, only a biological entity that would eventually become "me" the person.goodusername
September 18, 2013
September
09
Sep
18
18
2013
08:44 PM
8
08
44
PM
PDT
Phinehas, re. #43:
it is because the zygote/embryo/fetus is a human being from the moment of conception
To me, "human being" and "person" are pretty much synonymous. How do you differentiate between the two? In particular, how do you define "human being"?Bruce David
September 18, 2013
September
09
Sep
18
18
2013
08:33 PM
8
08
33
PM
PDT
To Elizabeth, If someone were to ask me "when did you begin to exist?" I can only arrive - honestly - at one answer: the moment I was conceived. At one point in my life I was that little conceptus...that little zygote. That was me 9 months before I was born. Everything in the universe has a starting point and I started the moment the sperm and egg became one. That's the old fashioned common sense answer and it is still good and valid. My being born was a necessary step in the "process" of my life....as was my entering puberty and then the later stages in life eventually. If one was to look at my baby pictures and then look at a recent picture one might see some similarities but they would have to look hard. But the baby pictures and the pictures of today are the same person. But I did not begin as a baby. "I" began at the moment of conception....that was "ME" at the very beginning of the "journey / process" of my life. Because if I didn't start there at the beginning, then I would not have hoped to exist at all.Johnnymack
September 18, 2013
September
09
Sep
18
18
2013
08:23 PM
8
08
23
PM
PDT
Now how did the writer in Psalm know to use the analogy of being knitted inside the womb?
"packaged like a spool of wound yarn"
Andre
September 18, 2013
September
09
Sep
18
18
2013
08:10 PM
8
08
10
PM
PDT
BD:
This is because you view the zygote/embryo/fetus as a person from the moment of conception. I do not, as I have said. Nor, I imagine, does anyone else who is pro-choice.
Actually, that's not quite correct. Rather, it is because the zygote/embryo/fetus is a human being from the moment of conception and I don't believe the notion that some human beings have different or less important rights than others is supportable from pretty much any perspective. Whether the zygote/embryo/fetus is a person or not is an interesting metaphysical question, but it is one that I don't think needs to be answered in order to see the logic in granting all human beings equal rights and in being especially resolute in protecting those rights for the most vulnerable.Phinehas
September 18, 2013
September
09
Sep
18
18
2013
08:03 PM
8
08
03
PM
PDT
Life Begins at Fertilizationbuffalo
September 18, 2013
September
09
Sep
18
18
2013
07:28 PM
7
07
28
PM
PDT
The egg or the sperm are alive but alone cannot create a new life. Once they meet a unique being is formed, on a journey to adulthood. "The process is astonishingly simple. In the embryo’s first moments, the Hox genes are dormant, packaged like a spool of wound yarn on the DNA. When the time is right, the strand begins to unwind. When the embryo begins to form the upper levels, the genes encoding the formation of cervical vertebrae come off the spool and become activated. Then it is the thoracic vertebrae’s turn, and so on down to the tailbone. The DNA strand acts a bit like an old-fashioned computer punchcard, delivering specific instructions as it progressively goes through the machine." “A new gene comes out of the spool every ninety minutes, which corresponds to the time needed for a new layer of the embryo to be built,” explains Duboule. “It takes two days for the strand to completely unwind; this is the same time that’s needed for all the layers of the embryo to be completed.” This system is the first “mechanical” clock ever discovered in genetics. And it explains why the system is so remarkably precise." Sourcebuffalo
September 18, 2013
September
09
Sep
18
18
2013
07:24 PM
7
07
24
PM
PDT
Elizabeth, re. #39: For once, Lizzie, we are in total agreement! :)Bruce David
September 18, 2013
September
09
Sep
18
18
2013
07:18 PM
7
07
18
PM
PDT
Bruce:
The claim that “life begins at conception” is patently false. The sperm and ovum are clearly alive well before they join to produce a zygote. This is code for “a person begins at conception.” But the anti-abortion movement is not honest enough to say it straight, for fear that the real issue would be glaringly apparent: at what point does a person come into existence?
This is exactly right. Not only are the sperm and ovum alive, but they are human, and indeed, a potential person. But not a person. When they meet, some extraordinary things happen, but not necessarily more extraordinary than the process that happened when they gametes themselves were formed (which was the point, interestingly, at which the proportions of grandparental sequences were fixed). Once a a particular pair of gametes meet, the combination of grandparental proportions on both sides is fixed. But there's still a long way to go before there's a person - at that point it isn't even determined how many people there are going to be. It is still a potential person (or people). A person is a lot more than a genetic sequence, or even a living human cell. If not, HeLa cells would be persons too.Elizabeth B Liddle
September 18, 2013
September
09
Sep
18
18
2013
06:51 PM
6
06
51
PM
PDT
cantor, re. #34:
In your considered opinion, Bruce David, at what point does that fertilized egg become a person, worthy of protection under the law… … and what non-religious-fundamentalist reasoning did you apply to arrive at that opinion?
The beginning of the third trimester. See #11, above. That said, I would want the law to be the result of consensus within the body politic, not a reflection of my personal beliefs. I suspect that that point would be viability of the fetus, but I don't really know.Bruce David
September 18, 2013
September
09
Sep
18
18
2013
06:35 PM
6
06
35
PM
PDT
Nice that a discussion of abortion came up in a post on DNA. And that after fertilization, the zygote (and so on) has DNA different from that of either parent. Perhaps we should compromise on a purely molecular means of deciding when a separate life has come into existence. (All I ask is give DNA a chance.)EDTA
September 18, 2013
September
09
Sep
18
18
2013
06:35 PM
6
06
35
PM
PDT
Phinehas, re. #32:
For me, however, this is like saying there are several things parents can responsibly do if they have a child: they can raise the child, they can put the child up for adoption, or they can kill the child.
This is because you view the zygote/embryo/fetus as a person from the moment of conception. I do not, as I have said. Nor, I imagine, does anyone else who is pro-choice.Bruce David
September 18, 2013
September
09
Sep
18
18
2013
06:27 PM
6
06
27
PM
PDT
Elizabeth Liddle:
buffalo: first of all, my comment was addressed to Mung whose post, possibly inadvertantly, seemed to imply that pregnancy could be avoided by the simple expedient of choosing not to have sex.
In spite of the fact that in the exact same post I also stated the following: No woman should be forced to have sex. Maybe, in whatever strange and wonderful world that Elizabeth inhabits, rape is not encompassed in that statement. NEWS FLASH ELIZABETH! Rape is not consensual!Mung
September 18, 2013
September
09
Sep
18
18
2013
06:22 PM
6
06
22
PM
PDT
In your considered opinion, Bruce David, at what point does that fertilized egg become a person, worthy of protection under the law... ... and what non-religious-fundamentalist reasoning did you apply to arrive at that opinion?cantor
September 18, 2013
September
09
Sep
18
18
2013
06:22 PM
6
06
22
PM
PDT
quite arbitrary determination that in their opinion a fertilized egg is a person
In your considered opinion, Bruce David, at what point does that fertilized egg become a person, worthy of protection under the law?cantor
September 18, 2013
September
09
Sep
18
18
2013
06:17 PM
6
06
17
PM
PDT
BD:
I never said people should not be responsible for their actions. There are several things a woman can responsibly do if she finds that she is pregnant: she can have the child and raise it herself, she can have the child and put it up for adoption, or she can have an abortion. None of these options, in my view, is irresponsible.
I think I understand your position. For me, however, this is like saying there are several things parents can responsibly do if they have a child: they can raise the child, they can put the child up for adoption, or they can kill the child. For me, one of these is not like the others. Parental responsibility generally means that parents cannot even neglect their children, let alone deliberately take action that will result in their death. For those interested in pro-life arguments that are not dependent upon religion, you might want to take a look at Libertarians for Life.Phinehas
September 18, 2013
September
09
Sep
18
18
2013
06:03 PM
6
06
03
PM
PDT
Phinehas, re. #23:
Just because sex, as created by God, is all of the wonderful things you’ve said about it and more, that does not mean it is or should be free of responsibility.
I never said people should not be responsible for their actions. There are several things a woman can responsibly do if she finds that she is pregnant: she can have the child and raise it herself, she can have the child and put it up for adoption, or she can have an abortion. None of these options, in my view, is irresponsible.Bruce David
September 18, 2013
September
09
Sep
18
18
2013
05:34 PM
5
05
34
PM
PDT
buffalo, re. #29:
The medical community does acknowledge life begins at conception.
The claim that "life begins at conception" is patently false. The sperm and ovum are clearly alive well before they join to produce a zygote. This is code for "a person begins at conception." But the anti-abortion movement is not honest enough to say it straight, for fear that the real issue would be glaringly apparent: at what point does a person come into existence?Bruce David
September 18, 2013
September
09
Sep
18
18
2013
05:28 PM
5
05
28
PM
PDT
Elizabeth - more the reason to err on the side of caution. The medical community does acknowledge life begins at conception. At the very least one must acknowledge this. Why deny the unborn, whose difference between you and I is time and where we live, the right to life, liberty and pursuit of happiness. It is simply a power issue. We have seen much of this before in the last century. For most cases abortion is used as a contraceptive. The rape cases you claim are really very infrequent.buffalo
September 18, 2013
September
09
Sep
18
18
2013
05:16 PM
5
05
16
PM
PDT
buffalo: first of all, my comment was addressed to Mung whose post, possibly inadvertantly, seemed to imply that pregnancy could be avoided by the simple expedient of choosing not to have sex. Unfortunately this is not the case. Secondly, like Bruce, I do not think it is a given that a conceptus/embryo/foetus is "a baby". I agree with Bruce that the idea of ensoulment at conception is a religious idea, and not even all religions agree as to when a foetus becomes a person. I don't entirely share Bruce's view, however, because I don't think there is a clear moment after which the foetus is a baby and before which it isn't. I think that becoming a person is a process, not an event. For that reason, I think that the later the termination, the weightier the counterbalancing reasons need to be to justify it. But that is why, in my view, the choice is one that should be ultimately up to the woman. I do think that attempts to stop women who have been raped from accessing emergency contraception on the grounds that what might have been an egg might now be fertised and thus in possession of a "soul" is, at the very least, to impose a purely religious belief on others, at the expense of their welfare. There is no science that can tell us when a fertilised egg becomes a person, and no good evidence that it is one from fertilisation. A fertilised egg has less neural activity than someone who is declared "brain dead".Elizabeth B Liddle
September 18, 2013
September
09
Sep
18
18
2013
05:08 PM
5
05
08
PM
PDT
Human Genome in Meltdown buffalo
September 18, 2013
September
09
Sep
18
18
2013
05:08 PM
5
05
08
PM
PDT
Of semi-related note: Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html "Sixty years on, the very definition of 'gene' is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level." (DNA at 60: Still Much to Learn April 28, 2013) http://www.scientificamerican.com/article.cfm?id=dna-at-60-still-much-to-learn Further Thoughts on the ENCODE/Junk DNA Debates - James Shapiro - Sept. 18, 2012 Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of "DNA Elements" rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries. Diogenes and like-minded people argue that we knew enough in the 1970s to understand the basic principles of genome organization. They do not accept that the flood of new information from genome sequencing and the kind of methodologies exemplified by the ENCODE project will fundamentally alter our genetic concepts. While they are certainly entitled to these opinions, I think we have to recognize that they are nothing more than that -- simply opinions that fly in the face of scientific history. http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html Of related note to the ID vs. Darwinism controversy, RNA’s are far more difficult to align into presupposed evolutionary trees than Genes are/were: micro-RNA and Non-Falsifiable Phylogenetic Trees - (Excellently Researched) video http://www.youtube.com/watch?v=qv-i4pY6_MU Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885 ----- Global project reveals just how active our 'junk' DNA is - Sept. 2012 Excerpt: Around 95 per cent of the genome appears to be very close to a switch, suggesting that almost all of our DNA may be doing something important. http://www.newscientist.com/blogs/shortsharpscience/2012/09/global-project-reveals-what-ou.html Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role - September 2012 Excerpt: The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said. There also is a sort of DNA wiring system that is almost inconceivably intricate.,,, ,,, Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect. http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all Verse and Music: Psalm 139:14 I praise you because I am fearfully and wonderfully made; MercyMe - Beautiful Lyric: Days will come when you don't have the strength And all you hear is you're not worth anything Wondering if you ever could be loved,,, http://www.youtube.com/watch?v=1vh7-RSPuAAbornagain77
September 18, 2013
September
09
Sep
18
18
2013
04:57 PM
4
04
57
PM
PDT
I'll throw this one in - Devout Catholics Have Better Sex, Study Says Group presents data showing those who go to church weekly have most frequent, enjoyable sex Join the club!buffalo
September 18, 2013
September
09
Sep
18
18
2013
04:56 PM
4
04
56
PM
PDT
Elizabeth Liddle - Mung, you are aware, are you, that pregnancy can result from rape? -------------- So how does a second crime, murdering a baby, mitigate the first. A good read - Why Can't We Love Them Both?buffalo
September 18, 2013
September
09
Sep
18
18
2013
04:54 PM
4
04
54
PM
PDT
BD:
Sex is one of God’s greatest gifts to us. At its best it is one of the most powerful, joyful, pleasurable, loving, and downright fun physical experiences we can have. And it turns out to be healthy as well! No one in this day and age should deny themselves this experience if they want it, be they male or female, married or unmarried, gay, straight, or bi. If a child is not wanted from the experience, then certainly it would behoove them to take the proper precautions, but if a pregnancy results, then an abortion can be chosen.
Just because sex, as created by God, is all of the wonderful things you've said about it and more, that does not mean it is or should be free of responsibility. The one does not follow from the other. A choice to have sex is a choice to accept the potential responsibility of parenthood. Trying to separate this consequence from the initial choice only ends in the victimization of progeny.
If you think sex is only for procreation, Mung, then don’t have any unless you want a child. But please don’t lay your morality on the rest of us.
I saw nothing to indicate Mung believes sex is only for procreation, nor has he made any sort of appeal to morality. This is a figment of your imagination arising from your non sequitur supposing that wonderful, pleasurable, and fun experiences must not have any responsibility attached.Phinehas
September 18, 2013
September
09
Sep
18
18
2013
04:48 PM
4
04
48
PM
PDT
You are welcome Bruce David. And Thank you in return.Ho-De-Ho
September 18, 2013
September
09
Sep
18
18
2013
04:31 PM
4
04
31
PM
PDT
Mung, re. #12:
I’m pro choice. No woman should be forced to have sex. If you don’t want to get pregnant, choose not to have sex.
Sex is one of God's greatest gifts to us. At its best it is one of the most powerful, joyful, pleasurable, loving, and downright fun physical experiences we can have. And it turns out to be healthy as well! No one in this day and age should deny themselves this experience if they want it, be they male or female, married or unmarried, gay, straight, or bi. If a child is not wanted from the experience, then certainly it would behoove them to take the proper precautions, but if a pregnancy results, then an abortion can be chosen. If you think sex is only for procreation, Mung, then don't have any unless you want a child. But please don't lay your morality on the rest of us.Bruce David
September 18, 2013
September
09
Sep
18
18
2013
04:28 PM
4
04
28
PM
PDT
1 2 3 4 5

Leave a Reply