A simple start?

_{Mark

October 20, 2009

Intelligent Design}

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In case we did not know, New Scientist confirms that at the base of the (postulated) tree of life is an extremely complex life form, much like a modern cell.

“There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.”

It is easy (or not) to imagine something as simple as that arising by natural processes.

here

Comments

born, I actually appreciated your thoughts in that last post--it gives us something to hang a potentially interesting discussion on. I'll be replying later whenb I have time. Probably the weekend.Dave Wisker_{October 30, 2009
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vjtorley, Many thanks for the link to the Cambrian article-- I have read Meyer's original article on information and the Cambrian Explosion, and it was nice to have another. I have done some thinking about the Cambrian Explosion, and will post it later when I have time.Dave Wisker_{October 30, 2009
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Thank you ladies and gentlemen. It is so good to have at least one thread going strong. Interestingly, the discussion demonstrates one of the basic tenents of Christianity. God does not force Himself on anyone. You will never find an absolute proof of God. What you find is just enough evidence if you are willing to believe, and not enough evidence if you do not want to. As one who made the transition from anti Christian to Christian at age 49 I can tell you how accurate that is. Not one thing in the universe changed when I opened myself to the possibility that Christ is God, but for the first time I saw how it all fits together. It really is a simple system composed of extradinarily complex parts and it works so well. We can find joy in the simplicity of the overall system and likewise enjoy delving into the most complex depths. But they all work because they are designed to work. My sympathies are with the deniers. Accepting Christ does mean accepting the need to change and act in a very specific manner (even though we usually have a difficult time living up to it). I did not want to accept that "control" either. Interestingly, the opposite has occurred. I am freer, happier, and more in control of my life. God Bless You All, GesualdoGCS_{October 30, 2009
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Well Dave, you know as I reflect on this, I realize that highly advanced algorithmic math must be "built" into every single amino acid used in life (a rather surprising finding which is staggering evidence for Design in and of itself), and to actually get the precise level of "algorithmic PID process control" that is conclusively shown to exist within the structure of the protein itself, the proteins must be "precisely sequenced" per each correct algorithmic amino acid to achieve the "specific algorithmic process function" of optimal functionality that we find in the individual proteins. I can assure you in the math exams I took using PID equations to solve process control problems, that using a "close" equation to solve a specific process control problem was not an option and was not an answer the instructor would accept. The answer was either exactly correct or it was completely wrong. So as it is in life, for instead of failing a test as I did a few times, the life-form most often dies for not being completely correct. And as Behe has elaborated on this week on ENV, there is now evidence that shows, that this "specificness" of process functionality, is present in "more and less" complex proteins of similar specific function. Thus supporting the strong inference that the "equations of algorithmic amino acids" must be specifically sequenced to achieve specific process control functionality. There simply is no other way to "engineer" this precise level of functionality. Now if Hunt actually wanted to do something of worth instead of chase his tail in a circle, he should try to figure out exactly which piece of algorithmic information is inherent in each amino acid so that we may actually try to construct correct mathematical models of protein functionality. That would be something I would buy him a beer for!bornagain77_{October 30, 2009
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born,
So Dave (And now Dave’s hero Mr. Hunt), to prove me wrong all you have to do is falsify Abel’s null hypothesis, which brings us back to square one does it not Dave? Actually, it doesn't. Square one is addressing Art's assessment of Axe's work, from which, since you steadfastly refuse to address them, we have never left.
Dave Wisker_{October 30, 2009
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Mr BA^77, I'm sure that if radio-telescopes ever detect lactic acid or lactose molecules floating in space, we will never hear the end of the stories like this! ;)Nakashima_{October 30, 2009
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vjtorley @ #320: When I call regulation by microRNA a low CSI proposition, I am following this outline of reasoning: 1. microRNAs (miRNAs for short) act by base-pairing to other target RNAs. 2. Target recognition is a matter of as few as seven nucleotides (see this essay for some more on this). 3. Some simple math shows that any seven-nt sequence will occur, randomly and by chance, fairly often in a eukaryotic genome, and that many, many more sequences are but one or two mutational steps away from being the target of a given miRNA. 4. If, as many (such as Glinsky) are assuming or claiming, miRNAs have a large impact on phenotype, it stands to reason that phenotype and phenotypic variation is well within the reach of random natural processes. 5. "Random, natural processes" seems to be the antithesis of CSI. Hence my assertion. I don't know why Sternberg might hold up microRNAs as examples of high-information moieties (if that is what he is doing - I haven't read his essay). If that is really where he is going, then he is wrong.Arthur Hunt_{October 30, 2009
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Actually Nak, since you claim to not believe in a Creator, you would have to write a paper of how the moon evolved into green cheese, instead of how it was "made" out of green cheese. LOLbornagain77_{October 30, 2009
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Mr BA^77, So I can write a web page about how the moon is made of green cheese, and links to 49 peer reviewed papers makes mine the equivalent of peer reviewed? But I see that in your next few messages, you are only quoting peer reviewed papers. Thank you.Nakashima_{October 30, 2009
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born, Art isn't my 'hero', but a longtime personal friend. I also happen to respect his professional work with RNA (which is the main focus of his lab).Dave Wisker_{October 30, 2009
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Look at the 49 peer reviews on the bottom of the first link NAK!bornagain77_{October 30, 2009
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Well Dave, Apparently Art thinks he has got all this figured out, so once again I ask why don't you guys send his paper to Axe? or at least get it published in peer-review? I saw a passing reference to me in which Art so graciously said I was "throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend," Well that is quite a statement from someone who failed to comprehend the fact that Junk DNA was not Junk nearly two years after ENCODE,,, As well I noticed that he flippantly blew off the staggering level of information inherent in a protein by trying ever so subtly to imply information could be had on the cheap,,, (nearly in one sentence did he ever so softly combine the two deceptions). Well now I guess that you guys will also have to send his paper to Abel since it seems our Mr. Hunt thinks he has found a way to falsify Abel's null Hypothesis for information generation,,, (If you want I will personally send it to Abel, so he made get a good laugh, and since you guys don't seem willing to let Hunt's paper get the scrutiny it truly deserves though you both jump up and down that it is "the truth" and primarily relevant, ignoring all contradictory evidence, just so to justify your atheism) I also would like to refocus on this I posted previously. that Mr. Hunt so graciously blew off by referencing my ignorance on the matter (as if he has a clue how this information generation occurs): Proteins have also been shown to have a “Cruise Control” mechanism, which works to “self-correct” the integrity of the protein structure from any random mutations imposed on them. Proteins with cruise control provide new perspective: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” Dave (and now the condescending Hunt) do you realize how much functional information is required to achieve a simple “process control loop” such as the dynamic cruise control loo we find in the proteinp?? Well lets take a look: For a protein to be “complete in its information content”, in its ability to “dynamically cruise control” it would have to implement three different algorithmic forms of information: Proportional (P) Integral (I) and Derivative. PID controller: Excerpt: A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller The equations involved for getting even this minimal level of “cruise control” for a dynamically interactive protein are staggering to put it mildly. (Page down on the wiki article to get a small taste of the equations I’m talking about) Several complex equations, which are derived from the basic PID platform of equations, are necessary to achieve different forms of simple process control, in different scenarios, in chemical industry. Many of these complex equations will surely be found to be integrated and overlapping. within the protein structure itself, so as to be utilized by the proteins in its "dynamic environment"(i.e. the information for "cruise control" must reside within the protein with no recourse to the DNA for correction once the protein is made). In such a demanding “process” as is found in life it is simply ludicrous to suppose the equations implemented within the protein structures themselves will be anything less than "tailor-made" for each individual protein. There is simply no other way for a protein to achieve such "sufficient" self-control, or any control at all for that matter, unless this type of specific "tailor made" algorithmic information is inherent within the structure of each individual protein… (I do have a college degree in process control so, contrary to Hunt's insinuation, I do have a clue what I'm talking about in this matter!) Shoot it is in realizing the staggering amount of engineering to individual proteins that this would require that I realize even the 1 in 10^77 estimate of Axe may be far to generous for finding a specific functional protein within sequence space. So Dave (And now Dave's hero Mr. Hunt), to prove me wrong all you have to do is falsify Abel's null hypothesis, which brings us back to square one does it not Dave?bornagain77_{October 30, 2009
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Mr BA^77, Want to match peer review Dave? Lets see I’ll match your 2005 paper with: There follows six links to non-peer reviewed web pages. So I'm not quite sure what 'match' means in your opening sentence.Nakashima_{October 30, 2009
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Dave Wisker (#317) Please convey my thanks to Art Hunt for his kind invitation to comment on his blog. I may do so, when I get a free moment. I was, however, intrigued by a comment which Art Hunt directed at bornagain77:
ba77, you are throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend, let alone address. One item is interesting, though. Specifically, the study you mention in #306 is actually a clever idea that strikes at the heart of a favorite ID notion - namely, that there is something called CSI (or FCSI) hidden inside of living things. The proposal discussed in the paper you cite explains how phenotype and its control is a decidedly low or zero-CSI proposition. I’m delighted that you would bring this to the attention of the Uncommon Descent crowd. (Emphases mine - VJT.)
Here's the link once again. Glinsky G.V. Phenotype-defining functions of multiple non-coding RNA pathways. 2008. Cell Cycle 7(11): 1630-1639. What puzzles me is that the same paper was cited by Dr. Richard Sternberg recently to support a very different conclusion. Sternberg is no fool, as I think everyone will acknowledge. In an article entitled How The Junk DNA Hypothesis Has Changed Since 1980 at http://www.evolutionnews.org/2009/10/ (scroll down to October 8, 12:39 p.m.), Sternberg writes:
Instead of 90% of the human or fly genome being junk, it seems that 90% or more of chromosomal DNA has some kind of specific developmental function, given the available data. Indeed, the emerging picture is that the species-specific nonprotein-coding regions encode numerous RNAs that help to shape the phenotype in ways that we are only beginning to understand.42 43 44 45 46 This is especially true for the transposable element fraction of human chromosomes—about 50% of our DNA—much of which is arranged and expressed in a taxon-specific manner. 33 47 48 49 Part of the reason for why a human is not a chimp is not a cow is not a whale, then, is that each species has its own set of sui generis "genes" — genomic texts specifying unique RNAs or even proteins that are used in embryogenesis. To put everything into perspective, I'll mine another quote from a paper worth reading:
We now know that more of the DNA in eukaryotic cells is copied into RNA than previously had been thought. Many of these transcripts serve regulatory instead of template functions in gene readout. Some of these newly recognized RNAs come from regions of the genome that had heretofore been deemed "junk DNA," yet no one could answer the obvious question: if "junk," then why still around? Before memory fades, we should note that there were some reasonably well articulated ideas 30-40 years ago that anticipated these recent discoveries.1
Indeed, those were the very same well-articulated ideas that the selfish DNA hypothesis was supposed to have dispensed with, once and for all. How things have changed since 1980. (Emphases mine - VJT.)
(The reference to Glinsky is #42.) "Zero-CSI"? Dr. Sternberg doesn't seem to agree. Hmmm....vjtorley_{October 30, 2009
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Correction: Also, as Clive has pointed out, atheists cannot provide a rational justification even for those things that they do condemn.StephenB_{October 29, 2009
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----seversky: “Is you God omniscient or not? If He is then he knows what we will do and why before we do it. So how can what we do make the slightest difference?” Just because God knows the future doesn’t mean that he impedes the activity of his creatures, or that his creatures cannot "make a difference." You are confusing omniscience with determinism. God knows whether or not the stock market is going to crash, but that doesn’t mean that he caused it to happen. God’s creatures possess free will, which means, of course, that they are liable to cause a lot of harm through dishonesty and greed, or, for that matter, they may do great things. God allows it all to play out. -----“No, if human life is precious because each one is unique and unrepeatable then none should be taken without a very good reason. I do not need a God to tell me that.” If that is the case, why do you hesitate to provide an unqualified condemnation of the destruction of innocent life in the womb? Indeed, why do you avoid the issue? The moral code that you have "worked out" doesn't seem to be up to the task. -----“You must be using a different fifth commandment. I do not get what you said from an injunction to honor your father and mother.” I was referring to “Thou Shalt Not Kill,” which is the fifth commandment in my Bible. -----“And, no ,atheism neither forbids nor requires anything. It is simply a lack of belief in a god. Atheists and agnostics in society, however, recognize that there are a number of things we should not do if we are to live together in peace and security. It is not so difficult to work out.” I once asked you to submit your moral code as a parallel to my moral code and proposed that you and I work out a integrated morality. You chose not to indulge me. If even two people cannot work out a moral code, how can six billion people work one out? They answer is that they can’t. The moral code must precede them. ----“You are evading the question. The dilemma lies in both patients needing treatment at the same time while there are insufficient resources to treat both; the point being that we are sometimes faced with choices where none of the alternatives are satisfactory. What would the good Christian do in such a situation?” Quite the contrary, I provided a specific, easy to understand answer. I said we take them as they come. What is it about taking them in order that you do not understand? If they come into the emergency room at exactly the same time, then the one whose life is in greatest danger gets priority, even if that person is old. For the atheist, the answer is equally clear—if there is a conflict of interest, then the old person must die. Here is a hint, by the way: Conflicts of interest always exist. That is why we need an objective moral code that transcends those conflicts. Our moral codes are different, which means that one of us must be right and one of us must be wrong. Indeed, everyone's self-styled morality is different from e everyone else's self styled morality, which is yet another reason for the need of a natural moral law that binds everyone, regardless of personal preferences. ---“As for survival of the fittest, it seems by some of the comments here about universal public healthcare that good Christians favor the private option which is much more a survival of the fittest system than the public option.” Incorrect. For what it is worth, there are two moral principles that apply to health care: The advanced principles of solidarity and subsidiarity, both of which are based on the basic moral law. But we have not yet elevated the discussion to that level as you don’t even believe in the natural moral law to begin with. So, you are not ready to discuss its more subtle corollaries. ----“Unlike some Christians, atheists and agnostics do not need a God to tell them that if they want their own right to life to be respected they must do the same for their fellows. -----“They can work that out for themselves. They can also agree that in a just and fair society, access to the necessities of life should be guaranteed to all.” But they haven’t worked it out as is evident from the fact that they kill babies without a qualm and are, as we correspond, planning to let old people die who are getting in their way. In a fair and just society, babies and seniors are not assassinated for the convenience of the ruling class. Indeed, you cannot even comment on the issue. So, clearly, you have not really "worked things out." Indeed, when atheists “work out a morality," they conceive one that is congenial with their individual inclinations, which means that they condemn sins they don’t commit and ignore sins they do commit. Hence, the atheist who steals will condemn violence; the atheist who fornicates will condemn cruelty of speech; and the atheist who slanders will condemn laziness---and so it goes. Also, as Clive has pointed out, atheists cannot provide a rational justification even for those things that he does condemn. If a man doesn’t conform his behavior to a moral code, he will find a moral code that conforms to his behavior. ----“Those societies that don’t see it that way tend to be those that subscribe to some sort of authoritarian and absolutist belief system, be it political ideology or religion.” Most societies all throughout history have been characterized by a master/slave relationship between the ruling class and its subjects. Political freedom is a rarity and the conditions that foster it are well known. Both atheists and religious fanatics militate against those conditions. If you are curious about the moral principles necessary for a well-ordered society, you can begin with “On Ordered Liberty,” by Samuel Gregg.StephenB_{October 29, 2009
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Art Hunt asked that I post this reply for him since he is still under moderation, and this discussion is preceding too rapidly for his replies to appear in a readable manner: Hi all, Many thanks to Dave for posting this in a timely manner. I'm delighted to see such an interest in the RNA Underworld. There is too much to respond to, so I'll try to focus on some bookends. Upright Biped at #283, the study you point to in an attempt to rebut my essay on junk RNA isn't particularly relevant to my essay. I was talking about things known as cryptic unstable transcripts. The study you cite was focused on relatively "un-cryptic" tiny RNAs. They are two rather different subjects, and the existence of tiny RNAs has no bearing on the fact that much (most) of the transcription products arising from highly-repetitive and other non-coding DNA end up in the garbage can. You are making an argument of the form: "The Yankess are better than the Phillies because Eli Manning is a better quarterback than Donovan McNabb." It doesn't make any sense, once you think about it for more than a second or so. ba77, you are throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend, let alone address. One item is interesting, though. Specifically, the study you mention in #306 is actually a clever idea that strikes at the heart of a favorite ID notion -namely, that there is something called CSI (or FCSI) hidden inside of living things. The proposal discussed in the paper you cite explains how phenotype and its control is a decidedly low or zero-CSI proposition. I'm delighted that you would bring this to the attention of the Uncommon Descent crowd. (Of course, the fact that the author's idea requires that the numerous small RNAs he mentions be expressed at some reasonable steady state level sort of makes the study irrelevant, at least when it comes to my essay on junk RNA. Hopefully, I won't have to explain what the word "cryptic" means.) Finally, vjtorley at #316, thanks for the kind words. Allow me to extend an invitation to you (and any other curious ID proponent) to ask questions about RNA, proteins, and ID at my blog. I'm afraid that the discussion here is moving faster than the SOM (Speed of Moderation).Dave Wisker_{October 29, 2009
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Dave Wisker (#296) I agree with you that Art Hunt's paper was an excellent one. Seldom have I seen such a lucid explanation of matters pertaining to biochemistry. I've just been having a look at Stephen Meyer's paper, The Cambrian Explosion: Biology's Big Bang which will be appearing as a chapter in Darwinism and Design soon. Here's the link: http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639 Pages 368 onwards make for interesting reading, as they address OOL issues. The Cambrian explosion is, in any case, orders of magnitude more difficult to account for than the evolution of life.vjtorley_{October 29, 2009
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Clive Hayden @ 264
And moreover, what compels us to choose between one system of ethics verses another? We cannot have an ethical duty for choosing an ethical system, for we are still in an ethical vacuum. And we have no way to compare between any ethical systems, because that would presuppose that we are recognizing a more ultimate ethical standard as our basis for comparison. What say you? If we were born tabula rasa, we would die tabula rasa
I take a pragmatic even - dare I say it - a scientific approach to ethics or morals, First, I look at them and ask what do they actually do? What is their function? What they appear to be are rules of behavior or codes of conduct that regulate the way people behave towards one another in society. The purpose seems to be to promote peace, stability and security - which makes sense regardless of your beliefs. And for agnostics and atheists, who believe this one life is all we have as ourselves, the wish is for as long and as enjoyable a life as possible. Respecting that wish in others is one of the best ways of ensuring that our own wish is treated with similar respect. In other words, our ethical and moral beliefs are rooted in - and arise from - our common needs as human beings.Seversky_{October 29, 2009
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Berceuse @ 262
Or uniquely absurd. For atheists, we are victims of a cosmic lottery, and to pretend like we are grateful for this is disingenuous in the face of a destiny of oblivion.
That was my point a little while back, that this need for gratitude makes no sense. I'm glad to see we agree on something.Seversky_{October 29, 2009
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vjtorley @ 258
Seversky I can see that the Flood troubles you theologically.
It does, because, as you rightly point out:
However, the notion that God might actually visit such a death upon innocent people – especially children – so that they ended their lives screaming in terror, is, I would agree, theologically scandalous.
That is putting it mildly. We might bow down before such a being out of fear for our lives but it would not be worthy of our worship. I do not believe that there is any evidence of the global flood as described in the Bible but the problem with the God of the Old Testament is that there are too many such incidents which force believers to resort to all manner of shifts and stratagems to find some sort of half-way acceptable way to account for them. Plainly, there is something wrong with that.Seversky_{October 29, 2009
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Bornagain, you are right one. These people still using the peer review argument are out of their ever loving minds. The bottom line is that you cannot critique a theory, saying it is not scientific because there are no, or now few, peer reviewed papers, while at the same time disallowing ID papers to be published in the first place. It is a self defeating philosophy to say something isn't sceince because it isn't peer reviewed, and that it cant be peer reviewed because it isn't science. Nonsense. ID is moving on whether these sworn enemies want it to or not- and not because of ID's "political pull"- as ID is disadvantaged politically and institutionally as it stands now- but it is progressing based on it's own merits and real value- especially regarding the promise of scientific fecundity.Frost122585_{October 29, 2009
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StephenB @ 255
The connection between this life and the next is more direct than you may appreciate. How you behave here determines in large measure how you will fare there.
Is you God omniscient or not? If He is then he knows what we will do and why before we do it. So how can what we do make the slightest difference?
Yes, and that isolated ethic causes the atheist to discount the preciousness of EVERYONE ELSE’S LIFE EXCEPT HIS OWN, except for those who may be of some use to him. Thus, babies, old people, or anyone else who gets in the way must die.
No, if human life is precious because each one is unique and unrepeatable then none should be taken without a very good reason. I do not need a God to tell me that.
Christianity declares that all life is sacred from the womb to the grave. The fifth commandment forbids all wanton violence against neighbor, both physical and, as it turns out, verbal. Atheism forbids nothing.
You must be using a different fifth commandment. I do not get what you said from an injunction to honor your father and mother. And, no , atheism neither forbids nor requires anything. It is simply a lack of belief in a god. Atheists and agnostics in society, however, recognize that there are a number of things we should not do if we are to live together in peace and security. It is not so difficult to work out.
For the Christian, both are of equal value, so both receive the same consideration. So, the doctor, and the health care system, takes them as they come in the order presented. For the atheist, the least fit must go—the sooner the better.
You are evading the question. The dilemma lies in both patients needing treatment at the same time while there are insufficient resources to treat both; the point being that we are sometimes faced with choices where none of the alternatives are satisfactory. What would the good Christian do in such a situation? As for survival of the fittest, it seems by some of the comments here about universal public healthcare that good Christians favor the private option which is much more a survival of the fittest system than the public option.
If there is no objective standard for morality to provide the dilemma, then there are no hard choices—only pragmatic choices. Hence, atheism, and the attendant pragmatism/utilitarianism are easy: Simply conduct a cost benefit analysis and kill those who can provide no return on the money invested by the state.
And what do you think private health insurance companies are doing now when they decide not to fund treatments? Unlike some Christians, atheists and agnostics do not need a God to tell them that if they want their own right to life to be respected they must do the same for their fellows. They can work that out for themselves. They can also agree that in a just and fair society, access to the necessities of life should be guaranteed to all. Those societies that don't see it that way tend to be those that subscribe to some sort of authoritarian and absolutist belief system, be it political ideology or religion.Seversky_{October 29, 2009
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Dave you still in 2007? Here is another 2009 peer review while I'm waiting for you to catch up:
Long noncoding RNAs: functional surprises from the RNA world. Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional "noise" as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell. http://www.ncbi.nlm.nih.gov/pubmed/19571179?ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
bornagain77_{October 29, 2009
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Seversky Why are you asking? Are you feeling the pain as the last vestiges of Junk DNA are crushed along with your ability to be a (ahem it hurts to write this,,,, fingers cramping,,, must write with knuckles) intellectually fulfilled atheist? Whew that was excruciating How to be an Intellectually Fulfilled Atheist (Or Not) http://www.amazon.com/How-Intellectually-Fulfilled-Atheist-Not/dp/1933859849 The slow, painful death of junk DNA: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work....Junk DNA is a necessary mathematical extrapolation...Without Junk DNA, evolution runs into insurmountable mathematical difficulties. http://creation.com/junk-dna-slow-deathbornagain77_{October 29, 2009
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bornagain77 @ 307
WOW Dave, This following paper blew Dawkins whole selfish DNA scenario clean out of the water,,,there ain’t even a “selfish gene” boat left to be seen anymore.
Just what did you think Dawkins meant by "selfish gene"?Seversky_{October 29, 2009
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WOW Dave, This following paper blew Dawkins whole selfish DNA scenario clean out of the water,,,there ain't even a "selfish gene" boat left to be seen anymore.
Altruistic functions for selfish DNA. - 2009 Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this "selfish DNA" or "junk DNA" dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo. http://www.ncbi.nlm.nih.gov/pubmed/19736519?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum
bornagain77_{October 29, 2009
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Hmm up to 2007 are we Dave: Phenotype-defining functions of multiple non-coding RNA pathways. 2008: Our analysis implies that hundreds thousands of non-protein-coding transcripts are contributing to phenotype-defining regulatory and structural features of a cell. Therefore, definitions of genes as structural elements of a genome contributing to phenotypes should be expanded beyond the physical boundaries of mRNA-encoding units. We propose an information-centered model of a cell suggesting that informasomes (the RNP complexes of sncRNAs and Argonaute proteins) represent the intracellular structures which provide the increasingly complex structural framework of genomic regulatory functions in higher eukaryotes to facilitate the stochastic (random and probabilistic) rather than deterministic mode of choices in a sequence of regulatory events defining the phenotype. http://www.ncbi.nlm.nih.gov/pubmed/18469518?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Hmm Dave... do you still think we should presuppose that if we don't know the function of Junk DNA fully that we should label it junk before all the facts are known just to placate your atheistic tendencies?bornagain77_{October 29, 2009
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Another paper to consider: Struhl K (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Structural & Molecular Biology 14: 103-105 From the abstract:
Eukaryotes transcribe much of their genomes, but little is known about the fidelity of transcriptional initiation by RNA polymerase II in vivo. I suggest that ~90% of transcriptional initiation in yeast represent transcriptional noise, and that the specificity of initiation is comparable to that of DNA-binding proteins and other biological processes. This emphasizes the need to develop criteria that distinguish transcriptional noise from transcription with a biological function.
Now some questions about the usRNA article to consider: 1. How are usRNAs formed? Are they transcribed from specific usRNA "genes"? Are they fragments generated by post-transcriptional processing (like intron-splicing), or byproducts of RNA degradation processing that acquired a function secondarily? 2. If they are individually and specifically transcribed, does each have its own promoter? 3. What percentage of the genome is talken up by the sequences specific to usRNAs, and how does that compare to, say, the percentage taken up by pseudogenes, inactive retroviral insertions, and other non-coding DNA? 4. Out of the thousands of usRNAs discovered by the John team, how many were actually found to have a function?Dave Wisker_{October 29, 2009
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---magnan: "It would be just as justified to ascribe belief in God to fear." ---"Aside from that, atheism can just as well be considered both an intellectual and an emotional position: that it is better to believe in no God, rather than a God ultimately responsible for the horrendous human condition (ignoring all the evidence for a Creator)." Both are emotional arguments, as you seem to acknowledge in parenthesis.StephenB_{October 29, 2009
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