Guest Post: Part 1 of 2: Qualitative Complex and Specified Information within genes – An Introduction

_{Barry Arrington

May 30, 2015

Intelligent Design}

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Today’s guest post comes to us from one of our regular commenters, Dr.JDD. All that follows is his:

I would like to start off this post by emphasising this is not meant to be seen in any way as a “disproof” nor an “attempt to disprove” the appearance of complex proteins in eukaryotic cells through proposed unguided evolutionary mechanisms. This is rather I hope something to stir up discussion and engage thought in particular to those who wish to understand better the real complexities and challenges that are needed to be overcome, if indeed we were to accept such proposed mechanisms as genuine and real.

We all know that mutations in DNA can result in a different amino acid appearing in a protein. For example the DNA triplet codon if read as “CTT” would be translated to the amino acid Leucine (L; obviously via the mRNA intermediate). However, if there was a mutation from the C to the G, the frame would read “GTT” and this would be translated into a Valine (V). As we all further know, we can have deleterious, neutral, and beneficial mutations (in a given context). Additionally, a mutation in the third letter of the DNA triplet codon is often redundant at the level of the amino acid because of the redundant nature of the genetic code (“perfectly optimised” many would say). Obviously then, removal of or insertion of a new DNA base will have a much greater impact on the sequence (as you will shift the reading frame) and therefore is usually deleterious.

Now I would make a request that I am not attacked for over-simplifying this concept, but to talk very simply about evolutionary change, mutations will occur at random in certain positions in the DNA sequence and this may be inherited (germline mutations) with a consequence of either deleterious, neutral or beneficial, with most “thought to be near-neutral.”

There remains a question though that has fascinated me for a while, and led me to look at some examples of this. What if we discovered other layers of code within the same gene? What would be the impact of a mutation on this other code, relative to the foremost code? How much would this then limit the availability of more than one code to co-evolve, realistically?

Now these are not questions I personally can easily answer nor have the capacity to answer, to any full degree. But I think it is something interesting that others who are perhaps smarter and of a more “code-orientated” training and mind-set should consider, especially in the context of the ID paradigm.

Just to make a “disclaimer” as well – I profess to not be an expert in this area. My PhD and some of my first post-doctoral work was in the endocytic pathway and protein trafficking and I then moved on to human Immunology. I am no longer in academia but rather the pharmaceutical world so the way I approach research and scientific questions is perhaps a little different than the academic approach, but personally I do not see that as a bad thing. I am not a geneticist is the main point I am making, although I obviously have some training in that field (not that this is an exceptionally useful thing).

Now with the advance of proteomics and our ability to detect peptides and “map” the human proteome, a lot of information has come to light. In particular, it is apparent we are “missing” a lot of proteins found in cells but not annotated as genes in our databases. Surprisingly, for quite some time the field has held to the dogma of one gene, one Open Reading Frame (ORF) – and potentially many different proteins due to alternative splicing events, for example. Yet recent studies mapping the human proteome (“A draft map of the human proteome.” Kim et al. 2014. Nature. 509, 575-581) have yielded many MS spectra that cannot be assigned to annotated genes in the human genome. With that publication in the prestigious Nature journal, one researcher made a very insightful comment which I would like to focus on (emphasis mine):

Xavier Roucou 2014 Jul 15
Among several significant contributions in this work, the discovery of 44 novel protein-coding open reading frames (ORFs) illustrates the complexity of the human proteome. Recently, we reported the discovery of 83,886 previously undescribed ORFs termed alternative ORFs (AltORFs) Vanderperre B, 2013. AltORFs are defined as ORFs present in the transcriptome that are different from annotated ORFs. We detected 1,259 proteins translated from AltORFs in human biological samples Vanderperre B, 2013. While the role and importance of this “alternative proteome” will require substantial further validation, there can be no doubt that a comprehensive description of the human proteome must include the distinct possibility of a vastly greater number of functional proteins than has been traditionally considered. Given the existence of the alternative proteome, it is not surprising that Kim et al. found that nearly 50% of the 35 million MS/MS spectra of human proteins did not match proteins in the NCBI’s RefSeq human protein sequence database. In an attempt to identify these novel proteins, the authors translated the human reference genome, RefSeq transcript sequences, non-coding RNAs, and pseudogenes. Among the 193 newly identified proteins, 44 were translated from novel uORFs, ORFs located in an alternate reading frame within coding regions of annotated genes, or ORFs located in 3’-UTRs. The astonishing failure to have detected the alternative proteome years ago results from the fact that MS-based proteomic methods rely on existing protein sequence databases that are far from complete and therefore do not allow the assignment of all MS/MS spectra. Recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals Ingolia NT, 2011 Lee S, 2012 Michel AM, 2012, and these alternative proteins should have been detected. In order to better define the human proteome, we generated a new database of alternative ORFs (AltORFs) present in NCBI’s RefSeq human mRNA sequence database. AltORFs overlap the annotated or reference protein coding ORF (RefORF) in an alternate reading frame, are located in the 5′- and 3′-UTR regions of an mRNA, or partially overlap with both the RefORF and an UTR region. This approach led to the discovery of 83,886 unique AltORFs with a minimum size of 40 codons Vanderperre B, 2013. The majority of mRNAs (87%) have at least one predicted AltORF, with an average of 3.88 AltORFs per mRNA. Additionally, the evolutionary conservation of many of these reading frames suggests functional importance. These AltORFs were translated in silico and included in an alternative protein database we used to interpret unmatched MS/MS spectra. So far, we and others have identified nearly 1300 alternative proteins in different human cell lines and tissues Vanderperre B, 2013, Klemke M, 2001 Oyama M, 2004 Vanderperre B, 2011 Bergeron D, 2013 Slavoff SA, 2013 Menschaert G, 2013, including certain of the 44 new proteins mentioned in the Kim et al. study: the alternative protein translated from the AltORFs mapping to the 5’-UTR of the SLC35A4 gene (or AltSLC35A4), was detected in Hela cells and lung tissue; the AltC11orf48 was detected in Hela cells, colon, lung and ovary tissues; and the AltCHTF8 was detected in Hela cells Vanderperre B, 2013. Twenty four of the 44 novel ORFs detected by Kim et al. were, in fact, already present in our AltORF database, and 9 of the 44 proteins translated from these novel ORFs were previously detected: AltASNSD1, AltSLC35A4, AltMKKS, AltSMCR7L, AltCHTF8, AltRPP14, AltSF1, AltC110rf48, AltHNRNPUL12. In this sense, Kim et al.`s study strongly supports the existence of the alternative proteome. Clearly, the alternative proteins detected by Kim et al. and by our team are the proverbial tip of the iceberg. A full map of the human proteome is thus still years away, and will require several important changes in our current thinking concerning the proteome and the concept that each mature mRNA only codes for one protein.

I could spend quite a long time talking about how fascinating this is, how little we know about proteins at present and how dogma has led us down a path to ignore an abundance of proteins just because they do not fit the standard model of thinking. It is truly amazing how little attention this line of work receives. For example, >90% of people I work with are PhD-level molecular and cellular biologists, and I have not yet met one who, when I have spoken of these things to them, is aware such layers of complexity exist. The dogma changes very slowly.

However what I wish to focus on are these AltORFs that are present in different reading frames of an already existing gene. Hopefully some of you will find this as utterly fascinating as I have. Hopefully some of you will even be able to think about the probabilistic implications to the evolutionary paradigm that this may (or may not) raise. I think most of us are fascinated by biology in one way or another so hopefully at least the first purpose will see some fulfilment.

As already discussed, a protein product is translated from an initial DNA code (via messenger RNA). This code is in triple – so 3 bases code for 1 amino acid, usually. However the reading frame is important. For example, consider the set of 3-letter words below:

THE CAT WAS NOT FAT

That makes sense and gives a message. Now let us change the way we read that by starting the 3-letter words from a reading frame shifted 1 letter over:

HEC ATW ASN OTF

What you notice is the message is completely lost – you cannot see any similarity to the first message, when looking at the triplets. Note – this is not one of those naïve attempts to use language to represent what happens with DNA code. That is different because in language you need to have particular combinations of letters to make the message viable. Whereas with DNA code, all you need are 3 of the four bases – any combination will give a message, either one of the 20 (usually) amino acids, or a stop code (or a start but that is the same as an amino acid, Met). That does not mean functionality of the polypeptide, but there is still a message. So this is just to illustrate you change the message – not you lose it!

Equally then, let us shift the reading frame over one again:

ECA TWA SNO TFA

All 3 messages are quite different. So what about with a DNA code and reading in different frames? Here is an example:

ATG CTT CAA TGC AGA TTC CCG GTT TCT TAG

Now ATG in DNA codes for the start codon and is a Methionine (M). TAG is one of several stop codons. So the translated result of such a code would be:

M-L-Q-C-R-F-P-V-S-*(STOP)

However, if you were to read in an alternative frame (shifted over 2 times from the original), you would see that starting at the 9th letter, we now observe a potential start codon of ATG appear:

(AT) GCT TCA ATG CAG ATT CCC GGT TTC CTT (AG)

This would then translate to (caveat – no stop codon here):

M-Q-I-P-G-F-L-…

As you can see, this looks quite different to the first peptidic sequence (ignoring the unavoidable starting Met). Given such a vastly different sequence, one may expect quite a different looking protein to be produced: a protein with different folds, structure and function (obviously this case is an example and neither sequence are long enough to be considered a “protein” as such but rather a short peptide, but this is merely to illustrate a principle).

So again, those that like to be fascinated by these things and consider paradigms let us consider a few things:

1) How does this affect the evolution of a protein when proposed to be through unguided processes?

2) What constraints are placed on apparent “neutral” or near-neutral mutations?

3) How does this affect the way you interpret an apparent “redundant” mutation in the DNA code?

4) Given the vastly different nature of the amino acid code (and thus strong chance of differing structure, folds and function), what are the probabilistic likelihood of such an alternative ORF (AltORF) encoding for a protein that plays a very close role with the common ORF it is found within?

Just to speak to some of those questions in particular with regards to points 1-3, I think broadly speaking this makes unguided evolution a lot harder. The reason being is any evolutionary changes to this region of overlapping ORFs in different frames means that a change has to be tolerated by BOTH proteins simultaneously. Where a mutation may have been neutral/near neutral before for the standard ORF now has to also be likewise (or beneficial) for the AltORF. As you are in a completely different reading frame, a conservative point mutation in the DNA code could very easily insert an aberrant stop codon for example into the AltORF. Suddenly, the layers are complicated (and this is just considering one single AltORF that overlaps). Thus without full understanding of the potential AltORFs present in a gene, one cannot simply state that a mutation is either a) neutral/near neutral/beneficial, b) redundant or c) conservative.

For example, in the above case we have as the 7th triplet in the original ORF, CCG which translates to a P (Proline). Let us say that we have a mutation from CCG to CCC – a single point mutation. This, in the original ORF is redundant – you still encode for a P. However, in the altORF that mutation has now changed a GGT to a CGT which is a Cysteine (C) to an Arginine (R). Those amino acids are not even close to being conservative (e.g. an L to a V might be considered a conservative change as these are both small hydrophobic residues). So you can see that the impact now of a single mutation which under the usual accepted paradigm of DNA code is seen as conservative or even redundant, suddenly becomes the opposite of this.

In part 2, I will try to review and summarise a paper that describes one such AltORF that overlaps with an existing normal gene, with implications in disease. Putting it into this context I think will help fascinate those of interest further, and also demonstrate some of the challenges unguided evolution must overcome.

Comments

Popperian @ 78 asserted,
Again, I’m not aware of any independent, first person accounts of his miracle.
Just to set the record straight . . . 1. There were many first-person accounts. Some were collected into a single corpus, but many of the witnesses, including all but one of the apostles were slaughtered in imaginative and cruel ways to suppress the “tribe of Christians” as Josephus termed them. Despite the holocaust against Jesus' followers, enough people survived to provide a continuous chain of trust across the centuries to the present. 2. You're confusing the kingdom of God with the Day of the Lord. They are completely different! The kingdom of God is a quiet but powerful divine sovereignty that authentic Christians cherish in their lives, resulting in the continuous power of God's forgiveness, transformation of their values, attitudes, and actions, and a profound inner peace. The power of the Holy Spirit arriving at Pentecost might also be alluded to. The Day of the Lord is God's direct intervention into humanity's destruction of themselves and the planet, and judgment of the nations. 3. The transliterated word in Greek is genea, which could mean race, family, or generation depending on context. Jesus said, “Truly I say to you this generation will not pass away until all these things take place.” Thus, in context, it seems that the Jews born around the same time as the terrible ecological disasters, wars, and genocides that Jesus had been predicting begin to happen, will not be wiped out as certain religio-political forces intend. But as I'm sure you agree, there are no forces in the world today committed to the destruction of the Jews, right? -Q Querius

Dr JDD
You have completely deflected, ignored and avoided my question. Rather, you have chosen to assume my line of reasoning, jump over the question asked and by predicting what you think I would say in response, use your rejection of that line of reasoning (I have not even made yet) as justification for not entertaining my questioning scenario.
First, I asked you where you disagreed, starting out with what i suspected was uncontroversial aspects of biology. That was a key point in my argument. However, the resurrection of biological life is not uncontroversial, regardless of who supposedly caused it. Second, my criticism was such that, regardless who supposedly performed the miracle or when it supposedly occurred, there are thousands of people who supposedly witness them. This is the case, even today. So, I didn't just jump over your question arbitrarily. I specifically did so to contrast claims of miracles and the sort of credulity many people exhibit towards them. That you accept some miracles, but not others, is relevant to the controversial point from which you started.
I really do not think you have studied very well the case for Jesus, unfortunately. I could spend pages replying to what you have said but it has been done to death elsewhere, and available for you to look into if you so wish. I suspect you do not want to know the truth.Sathya Sai Baba is a very different case. His critics deny his powers.
Actually, that's my point. Despite the differences, thousands of people believed Baba actually performed miracles. For Jesus to have genuine critics, there would need to be independent, first person accounts of his miracles. To my knowledge, no such independent, first person accounts exist.
Now, listen carefully. Not one of Jesus’ contemporary critics ever questioned if these miracles were real or not. At best, they interrogated a man and others around him to see if he really was blind from birth. But not once do we see them saying it was a trick, claiming that. In fact we are told they sought to kill him because he raised someone from the dead! Why? Because they hated His teaching and wanted Him gone as He taught against them, their authority and arrogance. The ones who sought to murder Him did not question his daily miracles. They attributed it to demonic activity, as that was the only way they could accept it without accepting His claim – that He was God incarnate.
Again, I'm not aware of any independent, first person accounts of his miracle. Second, many people believe in Baba's miracles despite his critics and despite the fact that he refused any kind of investigation. See the quotes in my original comment. Not to mention that supernatural intervention was commonly accepted at the time of Jesus. Robert Wright's The Evolution of God outlines how the supernatural beings were invoked to explain phenomena we simply did not understand. However, we no longer think lighting is the result of God's anger.
Sathya Sai Baba predicted he would not die until 2019.
Yet, there are headlines that read: Sathya Sai Baba’s Physical Death Prediction Comes True. How? His followers appealed to the possibility that Baba was referring to lunar years. Jesus predicted his return in the lifetime of his followers. Yet, Jesus' followers claim his prediction was accurate. How? They appeal to the possibility that what Jesus actually predicted was his transfiguration, not his return. Or that 'generation' actually meant 'race', or that “this generation shall not pass away” refers to the generation at the end time, or that “The time is near” and “coming quickly” is not in human scale, but God's scale. IOW, it's unclear why you accept rationalizations of Jesus' predictions, but not Baba's. Again, something simply doesn't add up. Popperian

Dr JDD [OT?] Here's a link to a post in another UD thread, which might shed some light on the current state of affairs in the ongoing 'evo-devo' debate: https://uncommondesc.wpengine.com/evolution/a-third-way-of-evolution/#comment-564085 Note that other posts in that same thread deal with the same subject too, but the above linked post references a very recent paper published in a peer-reviewed journal by authors who have been working on that subject quite a long time. When carefully reading research papers*, shouldn't we be very discerning and ask the most basic questions that may put the given paper to test? Perhaps the most fundamental question those papers should answer was popularized by a famous Wendy's TV ad: "where's the beef?" Also, those papers should meet a very important condition that was popularized by a famous Hollywood movie: "Show me the money!" :) (*) perhaps this includes a paper referenced @40 here in this thread? Dionisio

Kim et al: We identified eight cases where we observed peptides that mapped to an ORF located in an alternate reading frame within coding regions of annotated genes.
Dr.JDD: However what I wish to focus on are these AltORFs that are present in different reading frames of an already existing gene. Viruses are known to have proteins from alternate reading frames, but they seem to evolve without much trouble. See, for instance, Firth at al., Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses, Nucleic Acids Research 2014. Most alternative readings only form short peptides, and when they form proteins, they often don't fold. If an alternate reading leads to a functional protein, then gene duplication would allow decoupled evolution of each protein. Zachriel

Popperian, to answer now your second point (which did not answer my question but jumped straight over it):
So, why does should the supposed miraculous accounts of Jesus, of which took place thousands of years ago in the Palestine, become the basis for an entire world view, when we supposedly have miracles happening right now?Something just doesn’t add up.
I really do not think you have studied very well the case for Jesus, unfortunately. I could spend pages replying to what you have said but it has been done to death elsewhere, and available for you to look into if you so wish. I suspect you do not want to know the truth.Sathya Sai Baba is a very different case. His critics deny his powers. Investigating his life show contradiction in his claims to his reality - they question his motivations and activities, therefore they call into question his reliability and trustworthiness in many of the claims made. Did 1000s of people witness raising Walter Cowan from the dead? I think not. There is strong speculation this was fabricated. His critics have provided plausible explanations for his apparent “miracles” as being largely sleight of hand. Look at any modern magician and making something appear out of apparently nothing is quite easily done.What, however, is not easily done is to every day heal the sick, make people born blind to see, heal in front of people a man with a withered hand, heal the lame, and, raise a man who had been dead and stank of decomposition, from the dead.Now, listen carefully. Not one of Jesus’ contemporary critics ever questioned if these miracles were real or not. At best, they interrogated a man and others around him to see if he really was blind from birth. But not once do we see them saying it was a trick, claiming that. In fact we are told they sought to kill him because he raised someone from the dead! Why? Because they hated His teaching and wanted Him gone as He taught against them, their authority and arrogance. The ones who sought to murder Him did not question his daily miracles. They attributed it to demonic activity, as that was the only way they could accept it without accepting His claim – that He was God incarnate.I could make many other points about the history, the verification, the documentation, the reliability (Luke was perhaps one of the greatest historians ever to live) but it has been done over and over again elsewhere.What however, we must also remember about Jesus is that He lived His words, he predicted His death, and every prediction He made was true. He predicted the measure of the destruction of the temple in Jerusalem 40yrs before it happened. Sathya Sai Baba predicted he would not die until 2019. He failed that test. Sathya Sai Baba also has strong links to molesting young boys and possessed huge amounts of wealth, found after his death. Therefore we have many reasons to doubt that Sathya Sai Baba was who he claimed to be, and was just a good and convincing con artist that preyed on what people wanted and needed.Jesus however, was the exact opposite of what those people thought they needed and wanted. They wanted a king to take back their land and lead them as a conquering nation to rule the world. Jesus said He had to die and resisted being made a king – the crowds even tried to by force after he fed ~20,000+ of them. Further, we have very specific (and numerous) prophecies/predictions made about Jesus several 100 years prior to His birth which He fulfilled. Where are those specific prophecies about anyone else ever to have lived?So I ask you again, independent of what you think my next line of reasoning is, please answer my original question as I would like to know how you would interpret those events. Dr JDD

…ID proponents just don’t seem to care or even point out where they object, in detail. …I’ve mentioned it several times without any significant response…
Popperian, you are no doubt frustrated by the lack of direct response to your comments or questions posed to ID proponents, yet how can you expect significant response when you do not engage yourself with questions posed of you? You have completely deflected, ignored and avoided my question. Rather, you have chosen to assume my line of reasoning, jump over the question asked and by predicting what you think I would say in response, use your rejection of that line of reasoning (I have not even made yet) as justification for not entertaining my questioning scenario. As such, you avoid committing yourself to an answer that breaks down any hope we have of having a rational discussion about these things. My questioning was perfectly in line with how I can justify and interpret other lines of questioning (e.g. the one you are following through with me) from a personal point of view but you choose to ignore it and not answer it. So please do not complain about the actions of ID proponents when you are guilty of the same, as evidenced here. However, I am not one of tit-for-tat or recompensing like-for-like. So I will follow through your questions, if you find it useful (or entertaining).
– Saying that knowledge was previously located in one place (in an abstract designer) then copied to another (in organisms) does not explain the origin of that knowledge. It merely pushes the problem up a level without actually improving it. – As Popper pointed out, the more a theory prohibits, the better theory. Without some kind of limitations about the knowledge ID’s abstract designer possessed, when it possessed it, etc. one could appeal to ID’s designer to explain anything, including a biosphere that appeared to have evolved naturally.
Agree to a point. Where I differ is in the concept that the knowledge did not originate with the designer. So therefore what I am personally claiming/believe is that the origin of the knowledge is with the designer. You seem to be claiming that the designer was some sort of intelligent agent that passed on the knowledge by this statement. Tell me then, where did the origin of knowledge of how to build a computer come from? Of how to make a working watch? Are these not defined as coming from individuals? Or collections of individuals accumulating knowledge over time and piecing that knowledge together? If you say anything had knowledge but had to obtain it from elsewhere, you never solve the problem, as I believe you are saying. That is why when we see humans can innovate and be sources of knowledge, and we have good reason to believe a designer may design things that reflect their own attributes, we would conclude that a designer would be creative as well, i.e. be an originator of knowledge. Also known as the source of knowledge. So I would disagree that the designer has to have gained this knowledge from somewhere else. But I suppose you are coming onto the age-old question of “Who created God” which has been well discussed before, is a common fallacy and is of no worse position than any other theory described by any other human (just listen to Hawkins to see that – the universe can self-create, etc.). I agree. In and of itself, with no special revelation, a “god” can do anything and be anything you want it to be. Therefore on its own, a “god” is a rather substandard theory. So ask yourself this question – why do so many ID-supporters turn out to attach to a particular faith, often the Judeo-Christian origins of faith? Many argue that it was the chicken that came before the egg – religion drove them to choose ID and biases their view of the world. However the fact of the matter is that there are many where the egg came first. The natural world points to a designer, however this, as you say, is not a satisfying theory in and of itself. So therefore theology is turned to and without any revelation we are all just playing guessing games. So the question then comes to be, which revelation is true, if any? If you find one with strong evidence for truth, this can then reveal to you attributes about the designer that can be reapplied to the framework of scientific analysis and understanding observations. Now this will never be accepted by the scientific community as modern science has an a priori commitment to materialism and nothing but natural processes are capable of describing…natural processes! So it precludes the possibility of a designer (despite the theological aspect rooted in evidence itself, not on a whim). So I largely agree with what you write, especially, this:
the more a theory prohibits, the better theory.
The problem I have is two-fold (and I strongly suspect you will inherently disagree with this): The theory of evolution (macro/unguided UCD) accounts for every observation making it non-falsifiable thus little in difference to a “goddidit”. There have been many holes poked in the theory of evolution. Here with this OP I present a potential mountain that evolution has to climb and potentially one that is insurmountable with unguided processes in the proposed timescales (see part 2 when it comes out). This particular case needs more work to show that. But there have been many examples and mathematical models. Yet all evolutionary biologists roll over to the dogma and say that work is flawed. Having surveyed these arguments, including the contradictory nature of saying that truth is not selected for therefore things like self-awareness are illusions, it seems obvious to me that evolution is just as all-encompassing as theism. Even if evolution was much more restrictive than the design inference and so a “better” theory – that does not make it non-falsifiable and as per 1), when it is shown to fall short of what is necessary for it to be real, it must be dismissed. This is why there are the many members of “the third way” and other such movements away from neo-Darwinism. But, we do not see many hardcore atheistic evolutionary biologists even accepting the problems there are with this. That is telling. They downplay criticisms and refuse to rationally engage. They quote consensus thought and choose to perform character assassination rather than have a scientific discussion. In no other field within biology do you see such consistent and overwhelming lack of engagement with the criticisms. Yet that is exactly how science should progress: with null hypotheses and not relying on consensus. It seems philosophically obvious that people do not wish to reject Darwinistic evolution due to one’s worldviews and potential alternatives rather than where the science takes them. But this is the point – it should not matter what the alternative theory or theories are: if something cannot overcome the evidence and cannot explain the evidence, regardless of the alternative, it should be altered or dismissed. Even if in its current state it “prohibits more” as a theory. So ultimately we are not then pitting evolution vs ID. We are saying evolution fails. That does not mean ID wins. But ID is an alternative theory and until a better one comes about, it fits expectations. Dr JDD

Popperian:
So, why does should the supposed miraculous accounts of Jesus, of which took place thousands of years ago in the Palestine, become the basis for an entire world view, when we supposedly have miracles happening right now? Something just doesn’t add up.
LoL LoL Muwahaha LoL LoL Muwahaha Muwahaha Moron. [Someone had to say it.] Mung

Popperian: I’d also point out that ICEs are not replicators. They do not contain an internal set of instructions that indicate which transformations of raw materials should be performed to make copies of themselves. Nor do they appear out of thin air. They are most often made in factories, in which the knowledge of how to construct them is external. It’s unclear why this point totally escapes most ID proponents, as I’ve mentioned it several times without any significant response. Apparently, refusing to take theories they disagree with seriously considered an effective strategy for ID proponents? Which point? (a) not replicators? (b) no internal set of instructions? (c) not appearing out of thin air? (d) are most often made in factories? (e) the knowledge of how to construct them is external? Maybe the reason why "it's unclear" to you is that your argumentation is as clear as mud to us, referring to (a)~(e) above. I'm a trained engineer with advanced degree (although none in M.E.), AND a former Darwinian, so if you want to try again to tell us why self-replication excludes unfathomable genius and how we are somehow boneheaded to not to get it, please give it your best shot. I take it that you would accept the genius of the design of life if you could meet the genius in a corporate environment or read his story in the WSJ, or perhaps more likely Slate. Taking Darwinian theory seriously is not a problem for anyone on here I don't think; obviously that is the basis of this board. I take it seriously for drastically different reasons than when I believed it, after reconsideration for over 10 years. groovamos

A few notes on the overlapping complexity in DNA
Multidimensional Genome – Dr. Robert Carter – video (Notes in video description) http://www.metacafe.com/w/8905048 The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin https://vimeo.com/106012299 Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. 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 Duality in the human genome - Nov. 28, 2014 Excerpt: The gene, as we imagined it, exists only in exceptional cases. "We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel's time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,",,, "Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms.,,, http://medicalxpress.com/news/2014-11-duality-human-genome.html Design In DNA – Alternative Splicing, Duons, and Dual coding genes – video (5:05 minute mark) http://www.youtube.com/watch?v=Bm67oXKtH3s#t=305 Duons: Parallel Gene Code Defies Evolution. - Jeffrey Tomkins - 2014 Excerpt: Protein-coding genes—those containing the key information to make proteins—hold the most-studied type of genetic code. Some of the most important chunks of code in genes are the exons, which specify the actual template for protein sequences. In exons, three consecutive DNA letters form what is called a codon, and each codon corresponds to a specific amino acid in a protein. Long sets of codons in genes contain the protein-making information that ends up being translated into entire proteins that may be hundreds of amino acids in length. Before this study, scientists were aware that the protein-coding regions of genes had mysterious signals other than codons that told the cell machinery how to regulate and process the RNA transcripts (copies of genes) prior to making the protein. Researchers originally thought that these regulatory codes and the protein template codes containing the codons operated independently of each other. In reality, the new results showed that these codes actually work both separately and together. While one set of codons specifies the order of amino acids for a protein, the very same sequence of DNA letters also specifies where necessary cellular machinery (transcription factors) are to bind to the gene to make the RNA transcript that codes for a protein. As a result of this new discovery, these dual-function code sites in exons have been labeled “duons.” Scientists just last year reported that transcription factors clamped onto some exons inside genes but did not understand this dual code system until now.2 The human mind struggles to comprehend the overall complexity of the genetic code—especially the emerging evidence showing that some genes have sections that can be read both forward and backward.3 Some genes overlap parts of other genes in the genome, and now it has been revealed that many genes have areas that contain dual codes within the very same sequence.1,4 Even the most advanced computer programmers can’t come close to matching the genetic code’s incredible information density and bewildering complexity. An all-powerful Creator appears to be the only explanation for this astounding amount of seemingly infinite bioengineering in the genome. http://www.icr.org/article/duons-parallel-gene-code-defies-evolution/ Dual-Gene Codes Defy Evolution...Again. - 2014 Excerpt: Not only does a codon provide the information for which specific amino acid to add in the making of protein, but the variant of that codon influences the information needed on how to regulate its folding. Thus, you have two different sets of information encoded in different languages in the same section of DNA! The researchers state, “Dual interpretations enable the assembly of the protein’s primary structure while enabling additional folding controls via pausing of the translation process.” What was once thought only to be meaningless redundancy has now been proven to be exactly the opposite. In fact, the researchers say, “The functionality of condonic [sic] redundancy denies the ill-advised label of ‘degeneracy.’” per icr org What Is The Genome? It's Certainly Not Junk! - Dr. Robert Carter - video - (Notes in video description) http://www.metacafe.com/w/8905583 Comparing genomes to computer operating systems - Van - May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753 “Millions of DNA Switches That Power Human Genome’s Operating System Are Discovered.” - Sept. 2012 http://www.sciencedaily.com/releases/2012/09/120905135326.htm
bornagain77

Dr JDD:
And I also agree you push the problem of abiogenesis except I follow that through further than I suspect you do in that I believe the problem is pushed to a point that a naturalistic mechanism becomes implausible.
I've pushed the problem, in the context of my limited response, by merely proposing that material aliens did it. Nowhere did I present a theory about what does or does not represent the appearance of design, how it could be explained in a way that is comparable with no-design laws, etc., as indicated in the referenced paper. A such, we didn't end up with a better problem to solve than we started out with. Note: this is not to say I think an naturalist mechanism is impossible, but that I didn't provide one. Popperian

Dr JDD:
– a man dies, at least as can be verified through human observation (not machine) – the dead man is wrapped in grave clothes, not embalmed or had any procedure to avoid decay – the man is dead for 4 days – there is a stench from the body consistent with decay – another man commands a dead decomposing body to come out of the grave where the body has laid for 4 days – the man comes out, alive, no decomposition visible What would be a naturalistic explanation of those events? Let us assume he was truly dead and not in a coma?
First, the supposed life of Jesus was documented decades after it occurred. Nor is there any actual independent accounts to collaborate them. But even if that weren't the case, such claims are not enough to warrant their belief. Why? because many people attribute miraculous powers to people that live today. And they are so desperate to believe those powers exist the extent that they apply no criticism to supposed miraculous events on a regular basis. Example? Sathya Sai Baba supposedly miraculously and regularly manifested holy ash, jewelry and was even claimed to have raised the dead. Thousands of people supposedly witnessed these events first hand. And not just anyone. From the this CFI page on Sathya Sai Baba
In the documentary, T.N. Seshan, then chief election commissioner of India, held up a ring Baba gave him and said, “He gave this ring out of nowhere, which is set with nine gems; there is a ruby in it, a pearl in it, sapphire in it, there is an emerald in it, there is a diamond in it . . . he realized this for me out of nowhere.” Seshan later explained, “I am not a jumbly person. I’ve got a master’s degree in physics; I have a master’s degree in administration economics from Harvard. I find nothing contradictory between the physics and the fact that I believe this [ring] came out of the blue.”
Another example?
While Baba remained in the hospital, a miracle was proclaimed with followers and reporters flocking to see a four-foot wax figure of Baba “oozing perfumed oils from its feet” (Kumar 2011). The Times of India noted, “Devotees refused to consider that the wax idol could be melting in the sweltering heat and the oil was a resultant residue” (Kumar 2011). The same day, the Deccan Herald noted that the “idol stopped releasing the liquid after it was shifted to the ground floor of the residential complex” (“Axe Effect of Baba Wax Statue” 2011).
So, why does should the supposed miraculous accounts of Jesus, of which took place thousands of years ago in the Palestine, become the basis for an entire world view, when we supposedly have miracles happening right now? Something just doesn't add up. Popperian

Right.... but subfunctionalization (basically, an existing core function being split across multiple genes) is not "inadequate" to describe the first pattern (even if perhaps it won't be the right explanation when we look closer). If you argument is that we should invoke mechanisms that are capable of explaining observations as explanations for those observations then I guess we agree. But it doesn't add up to much... wd400

Mung:
I wonder how inefficient the internal combustion engine is.
Steel ICEs operate at 18 %-20 % efficiency on average.
Therefore not designed? Bad design??
From Wikipedia:
Most steel engines have a thermodynamic limit of 37 %.
So, they operate at an average of 85% of maximum possible efficiency. Mung:
Incompetent designer
Wikipedia:
There are many inventions aimed at increasing the efficiency of IC engines. In general, practical engines are always compromised by trade-offs between different properties such as efficiency, weight, power, heat, response, exhaust emissions, or noise. Sometimes economy also plays a role in not only the cost of manufacturing the engine itself, but also manufacturing and distributing the fuel. Increasing the engine's efficiency brings better fuel economy but only if the fuel cost per energy content is the same.
As I've been pointing out, variations around the thermodynamic limit of 37% can be explained a trade offs, based on human limitations, which includes limits on human knowledge. Electric motors are more efficient, but we lack the infrastructure to deploy them and the knowledge of how to build more efficient batteries. Also, the vast majority of electricity sources are themselves based on ICEs of some sort. Solar power is much more efficient, but we currently lack the knowledge of how to to replicate the efficiency as possible as well. IOW, we continue to use ICEs because we lack the knowledge to replace them en-mass without anoverwhelming cost that is greater than we would save. However, ID's designer is abstract and has no defined limitation to constrain it. This includes limits on resources, time or costs in rolling out entirely new infrastructure, etc. All ID can say is that biological organisms are as efficient as they are because, "That's just what the designer must have wanted.", which could be used to explain everything, which explains nothing. I'd also point out that ICEs are not replicators. They do not contain an internal set of instructions that indicate which transformations of raw materials should be performed to make copies of themselves. Nor do they appear out of thin air. They are most often made in factories, in which the knowledge of how to construct them is external. It's unclear why this point totally escapes most ID proponents, as I've mentioned it several times without any significant response. Apparently, refusing to take theories they disagree with seriously considered an effective strategy for ID proponents? Popperian

Dr JDD, OK, Going forward, here's where we will disagree. And we will disagree for philosophical reasons, not scientific reasons. Specially, we hold different epistemological views about what knowledge is, how it grows (or if it actually grows at all), etc., which you have not argued for, but merely implicitly assumed as theism is a special case of justificationism. ID's designer, by nature of being abstract and having no limitations, is an authoritative source of knowledge. This is, well, by design, as it allows a hole big enough to drive your preferred designer,
- Saying that knowledge was previously located in one place (in an abstract designer) then copied to another (in organisms) does not explain the origin of that knowledge. It merely pushes the problem up a level without actually improving it. - As Popper pointed out, the more a theory prohibits, the better theory. Without some kind of limitations about the knowledge ID's abstract designer possessed, when it possessed it, etc. one could appeal to ID's designer to explain anything, including a biosphere that appeared to have evolved naturally.
A designer that "just was", complete with the knowledge of just the right genes that would result in just the right proteins that would result in just the right concrete features, already present, doesn't serve an explanatory purpose. This is because one could more efficiently state that organisms "just appeared", complete with the knowledge of just the right genes that would result in just the right proteins that would result in just the right concrete features, already present. But, by all means, if you think ID has an explanation for that knowledge, then what is it? Note: I'm not suggesting the latter represents neo-Darwinism. Popperian

Thank you. That's my point. Rationalizing an observation with inadequate existing mechanisms, retards the potential for discovery. However, I don't disagree with you that looking to the familiar tends to be our first natural response. -Q Querius

It does not. wd400

wd400 admitted,
The results are surprising to be, because they suggest either (a) subfunctinalisation is more common than I thought (b) genes rapidly get tied up in networks (which doesn’t seem to be the case generally) (c ) a bit of both of these. It’s also conceivable that some other process explains these results, but being skeptical means weighing new evidence against what we already know.
How does subfunctionalization relate to the following? http://www.sciencemag.org/content/343/6172/769.abstract -Q Querius

Inefficient? Inefficient by whose standards?
"The brain of a small fruit fly uses energy in the micro-watts for complex flight control and visual information processing to find and fly to food. I don't think a supercomputer could yet simulate what the fruit fly brain does even while using megawatts of energy. The difference of over ten orders of magnitude and the level of energy used is an indication of just how incredible biological systems are. Professor Keiichi Namba, Osaka University http://www.youtube.com/watch?feature=player_detailpage&v=uw0-MHI_248#t=1645s Seeing the Natural World With a Physicist’s Lens - November 2010 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,, the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head;,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://www.nytimes.com/2010/11/02/science/02angier.html?_r=2&scp=1&sq=seeing%20the%20natural%20world%20with%20a%20physicist%27s%20lens&st=cse
Moreover, the ATP molecular machine is found to be 100% efficient (which blows comparable man-made machines out of the water in terms of efficiency):
Thermodynamic efficiency and mechanochemical coupling of F1-ATPase – 2011 Excerpt: F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,, Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase. http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1
As well the cell is found to be optimal in its metabolic efficiency:
Metabolism: A Cascade of Design - 2009 Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. http://www.reasons.org/metabolism-cascade-design Making the Case for Intelligent Design More Robust - 2010 Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites. http://www.reasons.org/making-case-intelligent-design-more-robust Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
In fact, optimal metabolism is found to be 'strikingly similar' across all life domains, thus strongly suggesting that all life on earth was Intelligently Designed with maximal efficiency in mind instead of reflecting a pattern of more or less random distribution that would be expected if Darwinism had occurred:
Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum Excerpt: Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet—from bacteria to elephants, and algae to sapling trees—we show that metabolism displays a striking degree of homeostasis across all of life. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572558/
ditto for photosynthesis:
Uncovering Quantum Secret in Photosynthesis - June 20, 2013 Excerpt: Photosynthetic organisms, such as plants and some bacteria, have mastered this process: In less than a couple of trillionths of a second, 95 percent of the sunlight they absorb is whisked away to drive the metabolic reactions that provide them with energy. The efficiency of photovoltaic cells currently on the market is around 20 percent.,,, Van Hulst and his group have evaluated the energy transport pathways of separate individual but chemically identical, antenna proteins, and have shown that each protein uses a distinct pathway. The most surprising discovery was that the transport paths within single proteins can vary over time due to changes in the environmental conditions, apparently adapting for optimal efficiency. "These results show that coherence, a genuine quantum effect of superposition of states, is responsible for maintaining high levels of transport efficiency in biological systems, even while they adapt their energy transport pathways due to environmental influences" says van Hulst. http://www.sciencedaily.com/releases/2013/06/130620142932.htm
bornagain77

bornagain77 quoted,
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously.
So, to use Dr.JDD's example, THE CAT WAS NOT FAT There might be an area where HASNT is included in the code: THE CAT WAS NOT FAT Thus if Trifonov is correct that there are 5-10+ overlapping codes in DNA, it would seem that any change might affect multiple genes. It would seem obvious then that overlapping codes would make DNA more compact at the expense of fragility and highlight the profound unlikelihood of any random change resulting in anything beneficial. It would also highlight the unlikelihood of an overlapping code evolving in the first place. -Q Querius

Popperian: Having quickly read over your series of statements I cannot particularly find anything I would say I contend with right now. And I also agree you push the problem of abiogenesis except I follow that through further than I suspect you do in that I believe the problem is pushed to a point that a naturalistic mechanism becomes implausible. Let me ask you a series of questions now : - a man dies, at least as can be verified through human observation (not machine) - the dead man is wrapped in grave clothes, not embalmed or had any procedure to avoid decay - the man is dead for 4 days - there is a stench from the body consistent with decay - another man commands a dead decomposing body to come out of the grave where the body has laid for 4 days - the man comes out, alive, no decomposition visible What would be a naturalistic explanation of those events? Let us assume he was truly dead and not in a coma? Dr JDD

Dr JDD:
However as you have just proven, materialists aren’t willing to entertain that idea but rather emphatically state as fact these things are inefficient.
Actually wd400 is right. They are inefficient. But that's hardly a point in itself. Evolutionary theory needs to explain why. Mung

Note that none of this suggests to wd400 that Darwinism could possibly be false! bornagain77

Why would natural selection favor inefficient cells? But it must have.
No. wd400

Your paradigm has just smothered an interesting finding with several speculations not based on any direct experimental evidence relating to the Drosophila findings.
Nah. I looked at new (to me) experimental evidence in the light of what we know about the world. Knowing something prior to reading a study is not the same as "smothering" the study's findings. The results are surprising to be, because they suggest either (a) subfunctinalisation is more common than I thought (b) genes rapidly get tied up in networks (which doesn't seem to be the case generally) (c) a bit of both of these. It's also conceivable that some other process explains these results, but being skeptical means weighing new evidence against what we already know. Again, it will be interesting to see how the fitness effects of mutations in new genes come about. wd400

“New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.” Shocked I tell you! Shocked! We were shocked! Mung

wd400:
I don’t know why you keep going on about materialism, but evolutionary biologists don’t make these claims. For one, eukaryotic cells are plenty inefficient as it is.
And I think this nicely illustrates some of the points. I wonder how inefficient the internal combustion engine is. Therefore not designed? Bad design? Incompetent designer? Why would natural selection favor inefficient cells? But it must have. Mung

wd400 retreated with,
It’s interesting, but why would you need “unknown meachanisms”. Subfunctionalisation (a classic model of gene evolution) should let to lots lethals in knockdowns of new genes. For other models of gene evolution you need only to have the new gene co-evolve with those in an existing network.
So why did you say that you were surprised? Your response quoted above is why I was surprised that you were surprised. Maybe my parenthetically excepting you was not a mistake after all. Your paradigm has just smothered an interesting finding with several speculations not based on any direct experimental evidence relating to the Drosophila findings. Again, why did you say you were surprised? -Q Querius

Dr JDD
This is just shifting goalposts and anyone with that view has the same problem. Namely, that any advanced intelligent agency confined to the observable time-space dimension contained within this universe still is subject to the same problem we are discussing here. Ultimately, the problem of natural abiogenesis.
You objected as I expected you would. All that does is push the problem of abiogenesis up a level without actually improving it, right? Yet, I've been pointing out that ID does the same thing. It merely pushes the problem of the origin of the knowledge found in organisms up a level without actually improving it. Yet, when I point this out, ID proponents just don't seem to care or even point out where they object, in detail. I'll illustrate why this is the case with a series of what we will both likely consider uncontroversial aspects of biology. Please indicate where in this series that you disagree. Perhaps you'll be the first to actually do so.
- Unlike cars or computers, organisms are not built in an "organism factory". Nor have we observed new organisms in recent history appearing out of thin air. Instead, organisms make copies of themselves. - As von Neumann pointed out, self-replication cannot occur without an internal recipe for how to perform the copy and a means of error correction to prevent an error catastrophe. In the case of biological organisms, self replication occurs when cells follow an internal recipe containing instructions of how to adapt raw materials such as air, water, etc. into copies of themselves. Cells contain discrete mechanisms that are reasonably effective enough against specific kinds of errors that can occur to, significantly more often than not, prevent a complete error catastrophe when copying its recipe. - The concrete features of an organism are a result of those transformations. Had an organism's cells contain a different recipe, it would have had different concrete features. Different organisms have different adapted concrete features because their cells contain different recipes.
With me so far? Again, I would think even you would find these aspects are uncontroversial, Right? if not, please indicate any objections you might have. However, as I continue, I suspect we may start to diverge somewhere below.
- An organism's recipe represent the knowledge of what transformations are necessary to result in an accurate copy of those organisms. Specifically, copies of organisms occur when the requisite knowledge of what transformations to perform are present in their cells. Again, organisms are not made in organism factories, where the knowledge of what transformations to perform would be external to the organism. Nor do organisms appear out of thin air by fiat. - As such, the origin of those features is the origin of the knowledge of what adoptions to perform.
Still with me? If not, where does your view differ and how? Popperian

wd400, you are the one who is just plain wrong in your claim that 'conservation of sequence' overrules observed functionality i.e. overrules ENCODE. Darwinists have yet to demonstrate the origination of a single gene and/or protein by unguided material processes, and yet you seem more than willing to claim that it is beyond all doubt that all species arose spontaneously from a common ancestor and therefore conservation of sequence determines functionality better than actual functionality determines functionality? That claim is beyond ludicrous! That claim is so wildly beyond what the evidence states it is 'not even wrong'. As Egnor stated in regards to Darwinian claims: A Neurosurgeon, Not A Darwinist - Michael Egnor Excerpt: "I read all that I could find. Johnson. Dawkins. Wells. Berra. Behe. Dennett. Dembski. What I found is this: The claims of evolutionary biologists go wildly beyond the evidence. "The fossil record shows sharp discontinuity between species, not the gradual transitions that Darwinism inherently predicts. Darwin’s theory offers no coherent, evidence-based explanation for the evolution of even a single molecular pathway from primordial components. The origin of the genetic code belies random causation. All codes with which we have experience arise from intelligent agency. Intricate biomolecules such as enzymes are so functionally complex that it’s difficult to see how they could arise by random mutations.... "The fight against the design inference in biology is motivated by fundamentalist atheism. Darwinists detest intelligent design theory because it is compatible with belief in God. "But the evidence is unassailable. The most reasonable scientific explanation for functional biological complexity–the genetic code and the intricate nanotechnology inside living cells–is that they were designed by intelligent agency. There is no scientific evidence that unintelligent processes can create substantial new biological structures and function."There is no unintelligent process known to science that can generate codes and machines. I still consider religious explanations for biology to be unscientific at best, dogma at worst. But I understand now that Darwinism itself is a religious creed that masquerades as science. Darwin’s theory of biological origins is atheism’s creation myth, and atheists defend their dogma with religious fervor. - Michael Egnor is a professor and vice chairman of the department of neurosurgery at the State University of New York at Stony Brook. http://www.forbes.com/2009/02/06/neurosurgeon-intelligent-design-opinions-darwin09_0205_michael_egnor.html bornagain77

Popperian complained,
The problem with Querius example is current race car “theory” is already well understood. As such, we have a relatively firm grasp of all the key problems that are associated with their operation and can perform an inventory or checklist of solutions that are needed to solve them.
This would imply that you're depending on a shroud of uncertainty in evolutionary explanations. The sports car engine is not understood by everyone, and history is replete with examples of reverse engineering. What I pointed out is the weakness in evolutionary speculation.
This would include a cooling fan, or some other means to dissipate heat. So, even before we start evaluating the car, we have a vast amount of knowledge we can utilize up front to identify functional components.
Which once again demonstrates the advantage of the ID paradigm---we're looking for advantages on the presumption of design rather than useless junk, vestiges of evolutionary development, or genetic drift.
Furthermore, racing is a highly competitive sport that hinges on hyper-efficiency. Unless it performs a compulsory role required to enter the race itself, such as safety or communications, we would not expect to find any significant components that have lost their function as they would unnecessarily increase the weight of the car.
Isn't evolution dependent on competition as well? :o
And we know what is necessary because, well, race car “theory” is already well understood.
As compared with evolutionary theory? Yes. Exactly. The ID paradigm is that it's likely that biological components that are poorly understood do have a purpose and are necessary to win the race for life. Disclaimer: I have not otherwise communicated with Popperian, nor is he my sock puppet. Everything he wrote was on his own initiative, not mine. -Q Querius

I don't know Q, this sounds like someone claiming something about conservation to me...
Evolutionary conservation is a highly misleading way to infer functional importance.
I see what you mean—there’s really no compelling evidence.
It's also just wrong. (It's not the only way to infer function, but no one has claimed that to be the case)
Yes. And it hasn’t been repeated by other labs and with other genes. Nevertheless, it still seems to have actually occurred, and there still must be an unknown mechanism involved.
It's interesting, but why would you need "unknown meachanisms". Subfunctionalisation (a classic model of gene evolution) should let to lots lethals in knockdowns of new genes. For other models of gene evolution you need only to have the new gene co-evolve with those in an existing network. It will be interesting to see how the fitness effects of mutations/deletions in new genes comes about, but it's not some dark mystery. wd400

Wd400 said,
That is a surprising paper, but it’s hardly evidence that phylogenetically recent genes are generally as important as ancient ones.
No, I don't think anyone is generalizing yet, but that something like this exists at all is astonishing, something which you also seem to acknowledge, which quite honestly surprised me.
It’s one experiment in one species with a handful (200) of genes testing only lethality of complete knockdowns.
Yes. And it hasn't been repeated by other labs and with other genes. Nevertheless, it still seems to have actually occurred, and there still must be an unknown mechanism involved. Ask yourself this. Does this discovery make you curious as to how it occurred, or does it make you rather wish this evidence would go away or be discredited? The paper you referenced is of course what one would expect and a valuable addition to our knowledge.
My comment had nothing to do with paradigms. You claimed that evolutionary conservation wasn’t a good predictor of biological function.
I wasn't “claiming” anything about evolutionary conservation---it was news to me as well. I was reacting to the discovery “that the importance of a gene have (sic) been shown not to correlate with its genetic age” and what it means. The problem with paradigms is that one can easily become stuck in one and not realize it. This applies to me as well as you.
. . . but if you are so insulated from the evidence that you can get something this wrong then I don’t know why anyone would bother with your opinion.
The irony has been noted. ;-) -Q Querius

photosynthesis is inefficient? care to cite? I certainly can cite evidence to the contrary! as to 'dead viruses": ERVs use to be a favorite of Darwinists to try to support common ancestry, but, in much the same fashion as new ORFan genes are found to be functional much earlier than thought, that claim was found to be false: Refutation Of Endogenous Retrovirus - ERVs - Richard Sternberg, PhD Evolutionary Biology - video http://www.youtube.com/watch?v=SrEOe2E0Euc Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116. Excerpt: Employing an information science model, the "functionalist" perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization. http://www.ncbi.nlm.nih.gov/pubmed/16093662 Shapiro and Sternberg Anticipated the Fall of Junk DNA - Douglas Axe - September 13, 2012 Excerpt: "In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function." These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written. The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful." - James Shapiro http://www.evolutionnews.org/2012/09/shapiro_and_ste064291.html Endogenous retroviruses regulate periimplantation placental growth and differentiation - 2006 http://www.pnas.org/content/103/39/14390.abstract. Retrovirus in the Human Genome Is Active in Pluripotent Stem Cells - Jan. 23, 2013 Excerpt: "What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. "In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn't found in any other cell types. http://www.sciencedaily.com/releases/2013/01/130123133930.htm bornagain77

. However as you have just proven, materialists aren’t willing to entertain that idea but rather emphatically state as fact these things are inefficient
There you go with "materialists" again... It's just true that many cellular processes are inefficient in eukaryotes. Our cells replicate dead viruses from millions of years ago, photosynthesis is inefficient, our polymerases could introduce fewer errors than they do, transcription produces abarent transcripts that our cells then have to go and mop up with various techniques... All I'm saying is that while we wait to learn how important alternative ORFs are, we should remember that simply detecting their products by MS is a long way from establishing a wide-spread role. wd400

Dr JJ:
That is, if someone were to observe let’s say as Querius suggests, a cooling fan, there are 2 simple theories. One theory is it looks like some distant functional component of a “related” transport machine it derived from and has lost function. Another theory is that it serves an important function in the sports car and that it is not a lost unnecessary feature.
The problem with Querius example is current race car "theory" is already well understood. As such, we have a relatively firm grasp of all the key problems that are associated with their operation and can perform an inventory or checklist of solutions that are needed to solve them. This would include a cooling fan, or some other means to dissipate heat. So, even before we start evaluating the car, we have a vast amount of knowledge we can utilize up front to identify functional components. Furthermore, racing is a highly competitive sport that hinges on hyper-efficiency. Unless it performs a compulsory role required to enter the race itself, such as safety or communications, we would not expect to find any significant components that have lost their function as they would unnecessarily increase the weight of the car. And we know what is necessary because, well, race car "theory" is already well understood. However, in the case of biological organisms, we do not have nearly the same vast amount of similar knowledge we can utilize up front to identify functional components. And we lack a inventory or checklist because we are developing theories about how those systems actually work, in detail, at the same time. That is, we have outstanding problems to solve in the case of biological organisms, which we have already solved in the case of race cars. Which brings me back to my comment about best practices for problem solving. Merely assuming something has an abstract purpose doesn't actually help us solve those problems. That's because abstract functionally cannot be found in conflict with empirical observations. Rather, we must first conjecture some concrete functional role for it to play. While observation are plentiful, good explanatory theories to explain them are not. Nor would we start out with the most complicated and difficult theories for us to test even if they were. When we find our theories wanting, are not merely wanting in some abstract way, they are wanting in very specific ways that constrain the way we approach the problem going forward, which gives us clues we didn't have before. Until then, assuming parts have some abstract function doesn't actually helpful, in practice. IOW, there is no practical difference between a component that we think plays no role in solving a particular problem and a component for which we have no concrete idea of what functional role it plays in solving that same problem. Neither of which can be actually used to explain anything in science. Popperian

wd400: Modern science is filled with examples of cellular processes that are deemed as we currently understand them to be, to be very highly efficient. Further, modern science has many examples of things in biology once thought to be quite inefficient yet when our understanding deepens we have found it was our misunderstanding rather than the reality. so while you may describe many cellular processes to be abberent and inefficient, I will prefer to sit on the fence and entertain the possibility that we just don't have a good understanding of them (and the cell as a whole) yet. I actually believe many findings in cellular biology support taking that view. However as you have just proven, materialists aren't willing to entertain that idea but rather emphatically state as fact these things are inefficient. Why? Because it fits nicely with their world view and to them pokes holes in the design inference. Low hanging fruit. Dr JDD

wd400 at 41 claims
"That is a surprising paper, but it’s hardly evidence that phylogenetically recent genes are generally as important as ancient ones. It’s one experiment in one species with a handful (200) of genes testing only lethality of complete knockdowns."
Yet, Fruit Flies are considered model organisms to test general principles of metazoans on, so it is hardly 'one species'. The authors themselves comment that the implications of their study could very well be important for human health:
"I think it has important implications on human health," Chen said. "Animal models have proven to be very useful and important for dissecting human disease."
As to the only a 'handful of genes' gripe of wd400, it is interesting to note the full context of the study that wd400 tried to downplay the significance of:
"But when nearly 200 new genes in the fruit fly species Drosophila melanogaster were individually silenced in laboratory experiments at the University of Chicago, more than 30 percent of the knockdowns were found to kill the fly. The study, published December 17 in Science, suggests that new genes are equally important for the successful development and survival of an organism as older genes. "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." The study used technology called RNA interference to permanently block the transcription of each targeted gene into its functional product from the beginning of a fly's life. Of the 195 young genes tested, 59 were lethal (30 percent), causing the fly to die during its development. When the same method was applied to a sample of older genes, a statistically similar figure was found: 86 of 245 genes (35 percent) were lethal when silenced. http://www.sciencedaily.com/releases/2010/12/101216142523.htm
The authors also comment in the main paper:
New genes in Drosophila quickly become essential. – December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract
Thus contrary to what wd400 tried to portray, the study's implications are hardly limited in scope. Of note to ORFan genes in general: The 'anomaly' of unique ORFan genes is found to be widespread. i.e. The 'anomaly' of unique ORFan genes is found in every new genome sequenced, taking up a fairly large percentage of each new genome sequenced:
,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.” Paul Nelson – quoted from 8:53 minute mark of the following video Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:
Estimating the size of the bacterial pan-genome Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,, also from the cite: Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf The essential genome of a bacterium - 2011 Figure (C): Venn diagram of overlap between Caulobacter and E. coli ORFs (outer circles) as well as their subsets of essential ORFs (inner circles). Less than 38% of essential Caulobacter ORFs are conserved and essential in E. coli. Only essential Caulobacter ORFs present in the STING database were considered, leading to a small disparity in the total number of essential Caulobacter ORFs. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202797/pdf/msb201158.pdf
Multicellular creatures have the same 'anomaly' of unexpectedly large percentage of new ORFan genes found in each new species sequenced:
Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf
Moreover, such a large percentage of unique ORFan genes were certainly not predicted by Darwinian theory and by all rights, ORFan genes should have falsified Darwinian theory. But Darwinists simply ignored the falsification that ORFans presented to their theory and moved right ahead as if their theory had not, in fact, been dealt a devastatingly fatal blow:
Proteins and Genes, Singletons and Species - Branko Kozuli? PhD. Biochemistry Excerpt: Horizontal gene transfer is common in prokaryotes but rare in eukaryotes [89-94], so HGT cannot account for (ORFan) singletons in eukaryotic genomes, including the human genome and the genomes of other mammals.,,, The trend towards higher numbers of (ORFan) singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea.,,, That hypothesis - that evolution strives to preserve a protein domain once it stumbles upon it contradicts the power law distribution of domains. The distribution graphs clearly show that unique domains are the most abundant of all domain groups [21, 66, 67, 70, 72, 79, 82, 86, 94, 95], contrary to their expected rarity.,,, Evolutionary biologists of earlier generations have not anticipated [164, 165] the challenge that (ORFan) singletons pose to contemporary biologists. By discovering millions of unique genes biologists have run into brick walls similar to those hit by physicists with the discovery of quantum phenomena. The predominant viewpoint in biology has become untenable: we are witnessing a scientific revolution of unprecedented proportions. http://vixra.org/pdf/1105.0025v1.pdf Is the Origin of New Genes “Basically a Solved Problem”? - Cornelius Hunter - Sept. 11, 2014 Excerpt: If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.” Case closed right? Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:,,, ,,,This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence. So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes must have evolved because solo genes are observed over and over: "Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.",,, Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.,,, Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved.,, http://darwins-god.blogspot.com/2014/09/is-origin-of-new-genes-basically-solved.html
Moreover, Darwinists have yet to actually demonstrate that unguided material processes can create even a single gene of those hundreds to thousands of new genes being found in each new species sequenced:
"Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way." - Doug Axe PhD - Nothing In Molecular Biology Is Gradual - video https://vimeo.com/118128889
bornagain77

Popperian: This is just shifting goalposts and anyone with that view has the same problem. Namely, that any advanced intelligent agency confined to the observable time-space dimension contained within this universe still is subject to the same problem we are discussing here. Ultimately, the problem of natural abiogenesis. So either you MUST be a materialist or you are a theist (where your theism recognises intelligence outside the confines of the observable universe). There really is no alternative. Even if you want to believe in a multiverse and somehow an advanced intelligent alien traversed across to our universe. You still have a problem of naturalistic abiogenesis to overcome. That is why you rarely hear the view you have proposed. It's logical conclusion makes you still choose between theism and naturalism. Dr JDD

Our materialist friends will however argue that they once were horribly inefficient (but provided benefit over even less efficiency before so selected for) it’s just that what we see around us now is the product of evolution: inefficiencies selected out. Which they claim is as predicted.
I don't know why you keep going on about materialism, but evolutionary biologists don't make these claims. For one, eukaryotic cells are plenty inefficient as it is. I have little doubt many of these altORFs will be aberrant, just like many alternative transcripts have turned out to be. As I understand it, most of these ORFs that have been validated are in UTRs where they may well be a kludgy way of controlling the timing/folding of translation of the primary transcript. There is certainly no requirement that a change provide a benefit in order for it to be fixed -- it only needs to make little or no difference to the host's fitness. wd400

Bornagain77 mentioned it in 3. Here’s the link so you won’t have to scroll up:
That is a surprising paper, but it's hardly evidence that phylogenetically recent genes are generally as important as ancient ones. It's one experiment in one species with a handful (200) of genes testing only lethality of complete knockdowns. More generally, young genes are usually smaller, involved in fewer networks and less effected by purifying selection (i.e. more mutations are tolerated). A recent paper on this last point, with repsect to gene expression in particular: http://www.ncbi.nlm.nih.gov/pubmed/25480033
A person’s preconceptions and chosen paradigm largely determines their perceptions and interpretation...
My comment had nothing to do with paradigms. You claimed that evolutionary conservation wasn't a good predictor of biological function. That's just wrong, I linked earlier to a paper in which phylogenetic conservation alone was shown to be a good predictor of a mutation's severity. You don't have to accept to evolutionary biology, but if you are so insulated from the evidence that you can get something this wrong then I don't know why anyone would bother with your opinion. wd400

Mung #35: But we are talking about codes here, and first we have to get them to admit that the codes actually exist, and not just as a metaphor.
Indeed. Our materialist friends, as Dr JDD calls them, can get really nasty about "code", "protocol" and so forth, but when I put it to them that, under materialism, there is no such thing as an "organism"—that it is just fermions and bosons—then they suddenly make a U-turn and pretend not to understand. Box

Mung:
But we are talking about codes here, and first we have to get them to admit that the codes actually exist, and not just as a metaphor.
Again, baffling, behavior. You'd essentially admitted to not reading the paper i referenced, which addresses that very issue. It's as if you think the answer has been revealed to you though some infallible source which is simply not subject to criticism. Popperian

Dr DD wrote:
Our materialist friends will however argue that they once were horribly inefficient (but provided benefit over even less efficiency before so selected for) it’s just that what we see around us now is the product of evolution: inefficiencies selected out. Which they claim is as predicted.
I find this kind of talk baffling. What does being a materialist have to do with it? Couldn't the designer just as well be a highly advanced, material alien civilization that seeded our planet with simple, inefficient replicators, as described in the paper I referenced, that gets natural selection going? Popperian

I’m sitting front row on this one. BTW I’m wondering how much AltORFs we humans share with chimpanzee/bonobo.
Exactly. Life has become increasing complex over time, and it will be very interesting to see how well these AltORF's map to that increase in complexity. But don't be surprised if humans and other primates share a great many of them. Mung

It seems obvious to me that the only way to go for the evolutionist is to deny the existence of other layers of code. AltORFs—on a substantial scale—is something that his theory definitely cannot accommodate.
I have to disagree with Box. That the theory is very accomodating has been shown time and again. Some people even think that's a strength of the theory. But we are talking about codes here, and first we have to get them to admit that the codes actually exist, and not just as a metaphor. The Organic Codes: An introduction to semantic biology http://www.codebiology.org/artcodetheory.html Life is not meaningless. Life was imbued with meaning from the beginning. Mung

Box, you will get no disagreement from me on your point! Our materialist friends will however argue that they once were horribly inefficient (but provided benefit over even less efficiency before so selected for) it's just that what we see around us now is the product of evolution: inefficiencies selected out. Which they claim is as predicted. So they can claim the eye is horribly inefficient which proves no designer then when we find it is near perfectly efficient in the way it is structured for its function, they can claim evolution has done an excellent job taking something efficient and selecting it to be inefficient. Heads they win tails you lose. Dr JDD

Dr JDD #32: (...) which again makes you wonder how such simple organisms could exist without efficient degradation components such as a proteosome or similar.
For such components to be "efficient", I would like to add, they must be incredibly fine-tuned. IOW exactly the incredible mind-boggling fine-tuning we see in 'modern' cells. Box

Hi Silver, Indeed which is why pseudogenes were much loved by materialists. Further, any odd translatable regions of DNA whose functions are unknown are usually labelled as "material for evolution to build from" as in our current understanding we cannot otherwise assign function. Yet time and time again we now are observing function. Take pseudogenes for example: many now are showing functionality. And not in the sense they are translated, but rather as regulatory RNAs that work via complementary sequences (thus just look like pseudogenes). I have never bought the ability of a cell to possess such scratchpads if you like, and as you say, just magically replace the old one or just add to the functional genome only when they are useful. Just study neurobiology and you will see what happens when you don't have a tight control on what types of proteins are translated or not. Aggregation is a serious problem to a cell's viability and functionality which again makes you wonder how such simple organisms could exist without efficient degradation components such as a proteosome or similar. Dr JDD

Dr JDD
For example, >90% of people I work with are PhD-level molecular and cellular biologists, and I have not yet met one who, when I have spoken of these things to them, is aware such layers of complexity exist.
ID looks at the bigger picture which makes it easier to see the many anomalies and conflicts in the unguided 'model' (if there is such a thing). I think the biologists are looking only at the micro-level, lost in the details (can't see the forest for the trees). You advised wd400 to 'take his head out of the materialist paradigm' and that basically says it. There's a simplistic, naive attempt to explain DNA mutations through gene-copying, with a redundant version acting like a non-functioning scratch-pad and the original, functional version remaining conserved until or unless the scratch-pad randomizations come up with something good. So, THE CAT WAS NOT FAT somehow (magically) remains impervious to mutational change and is (magically) conserved but the duplicate goes on mutating for a few million years until you come up with HAT ACT SAW TON TEF Then that fits right in place as a beneficial modification and it switches places with the original. :-) Silver Asiatic

Dr JDD @28, I'm sitting front row on this one. BTW I'm wondering how much AltORFs we humans share with chimpanzee/bonobo. Box

Dr JDD Very interesting article. Thank you. Here's a relatively recent paper that might serve as illustration for some of the ongoing discussions: https://uncommondesc.wpengine.com/intelligent-design/mystery-at-the-heart-of-life/#comment-566910 Dionisio

Box @24: Wait until you read part 2. I was literally blown away when I read about a code within a code that aligns to nothing else in the genome and actually functions as a protein that interacts with (and likely has functionality with) the main protein encoded by the traditional ORF. I honestly cannot conceive the likelihood of such processes arising through naturalistic unguided means nor understand how this can even be modelled to understand the probabilistic likelihood. Dr JDD

wd400 stated this
"Though, this other quote doesn’t give me much hope any of these comments are particularly attached to reality…"
in regards to this comment by Querius:
"I see what you mean—there’s really no compelling evidence. It’s simply an unproven assumption based on a faulty paradigm, circular logic, and ignorance."
Which Querius stated in regards to this observation,,
"So basically, for these Darwinists (critics of ENCODE), functionality did not determine if a sequence is actually functional, only ‘conservation of sequence’ determined what was functional. In other words, only if Darwinian evolution, (universal common descent), was assumed as true at the outset will Darwinists accept that a given sequence of ‘junk’ DNA may be functional! That is called ‘assuming your conclusion into your premise’ and is absolutely horrible science!"
That is a perfectly valid observation. And is completely 'attached to reality'. Darwinists always assume that Darwinian evolution is true at the outset of their investigation and never allow their theory to be fundamentally questioned or challenged. This dogmatic tendency of Darwinists to protect their theory from serious scrutiny is especially obvious in the ENCODE/Graur debacle.
Biological Information – (The Dan Graur incident) Criticizing ENCODE 12-13-2014 by Paul Giem – video https://www.youtube.com/watch?v=zhlFJO1WqVk
In this instance of finding widespread functionality for 'junk' DNA, the theory of universal common descent was used to determine whether the facts of widespread functionality, which ENCODE gathered by direct empirical observation, were correct.
Scientists go deeper into DNA (Video report) (Junk No More) - Sept. 2012 http://bcove.me/26vjjl5a Quote from preceding video: “It's just been an incredible surprise for me. You say, ‘I bet it's going to be complicated', and then you are faced with it and you are like 'My God, that is mind blowing.'” Ewan Birney - senior scientist - ENCODE 2012 ENCODE: Encyclopedia Of DNA Elements - video http://www.youtube.com/watch?v=Y3V2thsJ1Wc Quote from preceding video: "It's very hard to get over the density of information (in the genome),,, The data says its like a jungle of stuff out there. There are things we thought we understood and yet it is much, much, more complex. And then (there are) places of the genome we thought were completely silent and (yet) they're (now found to be) teeming with life, teeming with things going on. We still really don't understand that." Ewan Birney - senior scientist - ENCODE
The empirical facts about widespread functionality were not used to determine whether the theory of universal common descent was correct. What should be needless to say, theory, instead of experiment, dictating what facts are allowed to be considered is completely backwards as to how science is suppose to operate!
The Scientific Method - Richard Feynman - video Quote: 'If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.” https://www.youtube.com/watch?v=OL6-x0modwY
Of related humorous note, Dr Wells has developed a overarching 'assuming your conclusion' template for successfully writing a neo-Darwinian paper that never questions the assumption of neo-Darwinism:
Darwinian 'science' in a nutshell: Jonathan Wells on pop science boilerplate - April 20, 2015 Excerpt: Based on my reading of thousands of Peer-Reviewed Articles in the professional literature, I’ve distilled (the) template for writing scientific articles that deal with evolution: 1. (Presuppose that) Darwinian evolution is a fact. 2. We used [technique(s)] to study [feature(s)] in [name of species], and we unexpectedly found [results inconsistent with Darwinian evolution]. 3. We propose [clever speculations], which might explain why the results appear to conflict with evolutionary theory. 4. We conclude that Darwinian evolution is a fact. https://uncommondesc.wpengine.com/darwinism/jon-wells-on-pop-science-boilerplate/
bornagain77

BA77 #25, Very good choice of illustration for Popperian's style :) Box

Popperian, Dr JDD asks, 'Who are you referring to?' I'm asking "Exactly WHAT are you referring to?" You make such broad, disconnected, strokes with your personal opinions that it is like looking at a palette rather than a canvas when one reads your posts. http://www.arttherapyblog.com/uimages/2011/01/art-therapy-career2.jpg As I quoted earlier, ‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’ Berlinski bornagain77

Dr JDD: What if we discovered other layers of code within the same gene? What would be the impact of a mutation on this other code, relative to the foremost code? How much would this then limit the availability of more than one code to co-evolve, realistically? (...) I think broadly speaking this makes unguided evolution a lot harder. The reason being is any evolutionary changes to this region of overlapping ORFs in different frames means that a change has to be tolerated by BOTH proteins simultaneously. Where a mutation may have been neutral/near neutral before for the standard ORF now has to also be likewise (or beneficial) for the AltORF.
It seems obvious to me that the only way to go for the evolutionist is to deny the existence of other layers of code. AltORFs—on a substantial scale—is something that his theory definitely cannot accommodate. Box

Popperian: Who are you referring to? May I suggest something very simple (much like my car analogy was meant to be - illustrate a simple point with a common, simple example). That is, if someone were to observe let's say as Querius suggests, a cooling fan, there are 2 simple theories. One theory is it looks like some distant functional component of a "related" transport machine it derived from and has lost function. Another theory is that it serves an important function in the sports car and that it is not a lost unnecessary feature. Both are simple, testable feature. However if you favour one theory because it promotes your worldview, it stifles scientific progress. It is of no doubt that the attitude and commitment to junk DNA, and may I add the simplistic idea of a gene (as they fit with UCD and unguided evolution nicely) has therefore limited scientific research. so its not about foresight or over complicated theories, it's about being open to different theories regardless of the impact on.your worldview. Dr JDD

wd400, Bornagain77 mentioned it in 3. Here's the link so you won't have to scroll up: http://www.sciencedaily.com/releases/2010/12/101216142523.htm I was astounded, but I assumed that you wouldn't be.
Though, this other quote doesn’t give me much hope any of these comments are particularly attached to reality…
A person's preconceptions and chosen paradigm largely determines their perceptions and interpretations---as you and others continually demonstrate. I once believed in evolution, so it's easy for me to temporarily adopt that mindset, or find fault with it. But whatever. -Q Querius

Before a theory can be found in error by observations, you need to actually have a concrete theory, such as some percentage of genes actually are involved in expressing features in a particular way, such as directly coding for features. It's not helpful to merely assume all genes have some abstract functionality because that doesn't explain anything. Nor can merely serving some abstract function be criticized in hope of finding errors using empirical tests. Furthermore, we wouldn't start out by assuming some percentage of genes directly code for features, while some other percent modulate expression of those genes. That's because this idea only came about after conjecturing the idea that only some genes are directly responsible, noticing that theory has specific problems, in that it doesn't fully explain those features, conjecturing some other concrete way in the previous theory might be incorrect or incomplete, then testing that theory as well, etc. Nor is it clear how we could start from there, given that theories are not out there for us to mechanically derive from observations in the first place. We start out knowing they are conjectured, and therefore expect them to contain errors to some degree. So you might say theories are proposed, in a concrete way, for the explicit purpose of conflicting with reality. That's how we make progress. Theories are not merely wrong, they are wrong in very specific ways that constrain the way we approach the problem going forward. If you skip that step, where do you start looking? Not to mention it's unclear why you expect us to ignore best practices for solving problems. For example, you don't start out assuming the most complicated, convoluted and virtually impossible to test at the time theory, even if you somehow managed to have thought of it up front. Who actually does that, in practice? Rather, you start out with theories that can be excluded to get quick wins and help constrain future theories. For example, when debugging software, you don't start out by merely assuming the bug exists somewhere in the program. Where would you start looking: everywhere? No, you pick a possible cause for the problem that allows you to exclude the largest amount of the system with the least amount of effort, then try to exclude that as the cause of the problem. At which point you've significantly narrowed down the problem space. If that doesn't work, then you pick another potential cause that excludes the second largest amount of the system, with the second least amount of effort. And you repeat the process until you fix the bug. This is in contrast to simply randomly picking some possible cause, even if it takes two hours to generate a test file that allows you to exercise that part of the system, or requires you to travel to some other state to observe the program in operation. Yet, should we take the objections seen here seriously, that's essentially what you're asking researchers to do. How do you actually expect us to make progress? Then again, perhaps I'm being generous in assuming you actually want to solve problems in the first place. Popperian

What’s particularly astounding to everyone (except wd400) is that the importance of a gene have been shown not to correlate with its genetic age.
I would be surprised if this was true, do have a citation? Though, this other quote doesn't give me much hope any of these comments are particularly attached to reality...
I see what you mean—there’s really no compelling evidence. It’s simply an unproven assumption based on a faulty paradigm, circular logic, and ignorance.
wd400

First of all, what a interesting post, Dr. JDD. I very much appreciate your taking the time to write it up. Bornagain77 @ 3 expanded on Barry's comment on evolutionary conservation with the following:
Evolutionary conservation is a highly misleading way to infer functional importance.
I see what you mean—there's really no compelling evidence. It's simply an unproven assumption based on a faulty paradigm, circular logic, and ignorance. I liked your quote about “only” 8.2% of human DNA is functional and then a little further we get to read a quote that 10% of the human genome hasn't even been sequenced! That means that the 8.2% figure can only apply to the 90% known, and the .2% serves only to provide a false sense of precision. What's particularly astounding to everyone (except wd400) is that the importance of a gene have been shown not to correlate with its genetic age. Novel genes are just as likely to have a critical function as conserved ones. Things are getting curiouser and curiouser. The explanation for why the organism didn't go extinct before then will involve a lot of musta and mighta assertions. Dr. JDD's sports car analogy was great! I'd take it further by observing that while we're barely literate in sports car engines, some people are nevertheless adamant about the lack of function of the parts that they don't understand. They would vehemently argue that the cooling van is a vestigial aircraft propeller, or perhaps due to in-progress convergent car-volution, or perhaps only decorative. When an important function is later demonstrated for the cooling fan, and they are bludgeoned by the literature for a few decades, they accept it only with the greatest reluctance, and still insist that it constitutes only another 1% of the number of parts and that all the others are still non-functional! Thus, ever-so-slowly, various sects of evolutionists are dragged kicking and screaming down the road of scientific progress. Thanks again. -Q Querius

How come when I read one of your posts Popperian I am reminded of this quip from Berlinski?
‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’ Berlinski ‘Before you can ask ‘Is Darwinian theory correct or not?’, You have to ask the preliminary question ‘Is it clear enough so that it could be correct?’. That’s a very different question. One of my prevailing doctrines about Darwinian theory is ‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’ Nothing in the theory is precisely, clearly, carefully defined or delineated. It lacks all of the rigor one expects from mathematical physics, and mathematical physics lacks all the rigor one expects from mathematics. So we’re talking about a gradual descent down the level of intelligibility until we reach evolutionary biology.’ David Berlinski - EXPELLED - video (29:31 minute mark) https://youtu.be/V5EPymcWp-g?t=1768 Dr. David Berlinski: - extended interview - video playlist https://www.youtube.com/watch?v=hEDYr_fgcP8&index=2&list=PLF9DB30F6802BC5CE
bornagain77

Dr JDD, I am currently reading Code Biology: A New Science of Life. Very interesting stuff. BA77, Trifonov's work is mentioned a few times. Mung

Dr JDD,
Take for example all cars ever built. There are certain “conserved” parts. Given you usually always see a steering wheel, if assessing all the cars with no other knowledge of cars you could rightly predict that is probably an important component for functionality, broadly speaking. .
Human designers are the best explanation for human designed things. This is because human designers are not abstract and have defined limitations, such as finite amount of knowledge. Which, in turn, results in a finite amount of resources, time, etc. The specific kind of concrete common design we observe is explained by these limitations. Exotic cars have fewer common parts, but can take months to construct and cost significantly more to build. In contrast, today's automobile manufactures do not produce entirely new platforms every year because it would be too resource intensive to design, test and retool factories to build. We lack the knowledge to do so cost effectively. Consumers, who have limited resources, cannot afford them, etc. Adding extraneous parts would drive up the cost even more. However, in the future, human designers will have created the necessary knowledge to build entirely new vehicles inexpensively and efficiently. So much so, that they could build one-off cars for each customer sharing absolutely no common parts at all. And they will do so using advances in artificial intelligence, physics simulations and construction techniques based on today's 3D printers. For example, non-engineers will be able to design their own vehicles with the help of advanced artificial intelligence, which will be safety tested using advanced simulations and built just for them in their own garage. Eventually, the materials of an existing vehicle could be reused to reduce the cost even more. As such, the overhead of adding extraneous parts, or even non-standard controls, would be very low, should the user decide to add them on a whim. So, your argument breaks down, even in the case of human designers. In other words, your argument implicitly assumes we will not create the necessary significant knowledge to contradict it. This comes as no surprise as ID proponents grossly underestimate the role that knowledge plays in design.
The observation of “conservation” however is entirely consistent with a common designer and reuse of blueprints much like we see shared blueprints for cars.
Actually, it's not. This is because ID's designer is abstract and has no defined limitations. As such, it has no limits what it knows, when it knew it, etc. In turn, it has no limits on resources, time etc. to act as a constraint for reuse. Nothing but the laws of physics would constraint it, if even that, as it supposedly designed those as well. Eventually human designed things will have considerably less in common, despite humans being finite. So, for ID's designer to be consistent, it would have to become considerably less abstract by nature of positing concrete limitations to constrain it. However, that's simply not going to happen. ID's designer is abstract, by design. Popperian

Thirty Years of Multiple Sequence Codes - Edward N. Trifonov - 2011 How Many “Second Genetic Codes”? Excerpt: According to the media sympathetic to science and enthusiastic about sensational discoveries, the “Second Genetic Code” as it was called by New York Times (8) was discovered by Ya-Ming Hou and Paul Schimmel and published in Nature in 1988 (9). It was about recognition of tRNAs by respective aminoa- cyl-tRNA synthetases. Thirteen years later New Scientist announced the second Second Genetic Code (13), discovered by Jenuwein and Allis (14) and published in Science. This time it was about histone modifications. Five years later, New York Times, again, reported about “a second code in DNA in addition to the genetic code” (15). This was already the third Second Genetic Code, discovered by Segal et al (16), sug- gesting now nucleosome positioning rules. One, surely, would raise eyebrows having learned that there is also the fourth Second Genetic Code (17)—on in- teraction specificities between proteins and DNA, and the fifth Second Genetic Code, the name given by Nature magazine (18) to the set of rules governing gene splicing(19). Bewildered reader, naturally, would say “I’m done with seconds, can I have a third?” (20) The conclusion from the above is obvious: one has to admit that the genetic sequences carry many different codes. If we are to know what the sequences are about, we have to detect and decipher these codes. The times of surrender to “junk” and “selfish DNA” are over, and “non-coding” becomes a misnomer.,,, http://www.sciencedirect.com/science/article/pii/S1672022911600016
At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark): "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 Here are some more notes on overlapping coding:
Multiple genetic codes Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code. Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins:,, chromatin code (Trifonov 1980) RNA-to-protein translation code (triplet code) framing code (Trifonov 1987) translation pausing code (Makhoul & Trifonov 2002) protein folding code (Berezovsky, Grosberg & Trifonov 2000) fast adaptation codes (Trifonov 1989) binary code (Trifonov 2006) genome segmentation code (Kolker & Trifonov 1995) The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered. http://en.wikipedia.org/wiki/Edward_Trifonov#Multiple_genetic_codes The multiple codes of nucleotide sequences. Trifonov EN. - 1989 Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). http://www.ncbi.nlm.nih.gov/pubmed/2673451 Trifanov EN - Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. - 1997 Excerpt: The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages. http://www.garfield.library.upenn.edu/histcomp/alberts_na-auth-citing/node/6766.html Codes of biosequences - E. N. Trifonov - 2007 http://is.muni.cz/el/1431/jaro2007/Bi_IB8/Codes_of_biosequences.pdf Multiple levels of meaning in DNA sequences, and one more. - Trifonov EN, Volkovich Z, Frenkel ZM. - 2012 Excerpt: If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code. Nucleosomes preferentially are located at the ends of exons, thus protecting splice junctions, with the N9 positions of guanines of the GT and AG junctions oriented toward the histones.,, http://www.ncbi.nlm.nih.gov/pubmed/22954214
bornagain77

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Overlapping Genetic Codes 12-6-2014 by Paul Giem - video https://www.youtube.com/watch?v=3WZy0n60_ZU In the book "Biological Information: New Perspectives" Chapters 6 and 9 (at least) argue that stretches of DNA can have multiple functions encoded into them. We will partially evaluate the strength of the evidence behind that argument. 1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Book available in sections at http://www.worldscientific.com/worldscibooks/10.1142/8818#t=toc 2. Kapranov P., et al. 2005. Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172043/ 3. Birney E., et al. (Encode Project Consortium) 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. Available at http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html 4. Itzkovitz S., Hodis E., Sega E. 2010. Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. Available at http://www.ncbi.nlm.nih.gov/pubmed/20841429 5. He H., et al. 2007. Mapping the C. elegant noncoding transcriptome with a whole genome tiling microarray. Genome Res 17:1471-1477. Available at http://www.ncbi.nlm.nih.gov/pubmed/17785534 6. http://www.mcld.co.uk/hiv/?q=HIV%20genome 7. http://nsmn1.uh.edu/dgraur/niv/sabath_phd_thesis.pdf
etc.. etc.. etc.. bornagain77

With the advance of science, and with the revealing of more and more astonishing, even unbelievable, levels of extremely sophisticated integrated complexity being found in the genome, I find the Darwinian belief that the vast majority of the genome is junk to be a sure mark that Darwinists have completely lost any semblance of rational objectivity in their analysis of the evidence. IMHO, for Darwinists, the Darwinian paradigm takes precedence no matter what the evidence may say to the contrary. They simply completely refuse to entertain the thought that Darwinian evolution may be false. Here are a few notes as to the astonishing complexity being dealt with:
DNA - Replication, Wrapping & Mitosis - video http://vimeo.com/33882804 Dr. Jerry Bergman, "Divine Engineering: Unraveling DNA's Design": The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million. http://www.harunyahya.com/books/darwinism/if_darwin_had_known/if_darwin_had_known06.php#dipnot 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009 Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm Biochemical Turing Machines “Reboot” the Watchmaker Argument - Fazale Rana - July 2012 Excerpt: ,,DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency. per steve brown net Information Storage in DNA by Wyss Institute - video https://vimeo.com/47615970 Quote from preceding video: "The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA." Sriram Kosuri PhD. - Wyss Institute Ten years on, still much to be learned from human genome map - April 12, 2013 Excerpt:,,,"What we've learned over the past 10 years is that we're still far from really understanding the complexity of the human genome," said Eric Schadt, chairman of genetics and genomic sciences at Mount Sinai Icahn School of Medicine in New York City. "Human disease is way more complicated than the old view that single hits to single genes cause diseases. "In most forms of diseases, it's whole constellations of genes operating in networks," Schadt explained. "That becomes a much harder problem. How do you target networks with a single drug?,, (Or vice versa, how do single mutations to single genes incrementally build "constellations of genes operating in networks" in the first place?),,, "We keep learning how much we really don't know and how much further we need to go," he added. "That's the big story.",,, What's more, about 10 percent of the human genome still hasn't been sequenced and can't be sequenced by existing technology, Green added. "There are parts of the genome we didn't know existed back when the genome was completed," he said.,,, http://medicalxpress.com/news/2013-04-ten-years-human-genome.html The Complexity of Gene Expression, Protein Interaction, and Cell Differentiation - Jill Adams, Ph.D. - 2008 Excerpt: it seems that a single protein can have dozens, if not hundreds, of different interactions,,, In a commentary that accompanied Stumpf's article, Luis Nunes Amaral (2008) wrote, "These numbers provide a sobering view of where we stand in our cataloging of the human interactome. At present, we have identified less than 0.3% of all estimated interactions among human proteins. We are indeed at the dawn of systems biology." http://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575
bornagain77

Barry
Why would evolutionary conservation necessarily predict functional importance? After all, we constantly hear that evolution also accounts for vestigial organs and junk DNA (not so much the latter anymore).
Why? Because neo-Darwisnism falls under the same umbrella as our current, best universal explanation for how knowledge grows. Specifically, theories are not out there for us to mechanically derive from observations. As such, explanatory theories are essentially guesses about how the world works, which are not guaranteed to actually solve the problems they are proposed to solve. For the same reason, we have no guarantee that those same theories will not solve other problems they were not conjectured to solve, either Even in the case of human designers, functional importance isn't guaranteed to occur, regardless of our intention to bring it about. When it does, it's the idea or functionally itself, in that solves some problem, that is key, not the original problem or the source. So, your question is based on a specific epistemological view you hold, not evolutionary theory itself. Note: I'm not a ID proponent because I've failed to take into account what we know about human designers. Rather, I'm not a ID proponent precisely because I've taken what we know about human designers into account. Intention simply isn't sufficient. Popperian

wd400 claims that: "For instance evolutionary conservation and nothing else (phyloP) is a pretty good predictor of how bad a mutation will be in humans" Actually where mutations are most likely to be 'always catastrophically bad' are in the regulatory regions where 'orders of magnitude' differences are found between species.
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F "Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes." Raymond Bohlin (per Richard Sternberg) - 9:29 minute mark of video https://vimeo.com/106012299 A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html Darwin's Doubt (Part 8) by Paul Giem - developmental gene regulatory networks and epigenetic information - video http://www.youtube.com/watch?v=rLl6wrqd1e0&list=SPHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&index=8 How to Build a Worm - Paul Nelson - video https://www.youtube.com/watch?v=QDQ0NJQ_z3U Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/
Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be 'always catastrophically bad'. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial, ‘orders of magnitude’, differences are found between even supposedly closely related species. Needless to say, this is the exact opposite finding for what Darwinism would have predicted for what should have been found in the genome. bornagain77

Hi Mung, Thanks for your comments. In part 2 I go through a case example from the literature and it seems to be conserved at least among higher mammals. Interestingly while the typical protein shows high homology (80-odd % to mouse if I recall correctly) however the predicted altORF in the same gene (different frame) is as low as 30-odd % homologous. It's an interesting example and curious to know how widespread it is. Dr JDD

Thanks Dr JDD. I suppose that conserved regions might be a good place to look for overlapping genes. Another approach could involve identifying overlapping regions and then looking to see whether they are conserved, and if so how far back in time that seems to have been the case. Mung

Right, but that was in answer to Barry's question, where he seems to think claiming conservation is correlated to function is contradictory to claiming evolution can create junk DNA. You might not like that particular argument for junkiness of our DNA, but it certainly doesn't contradict the correlation between conservation and function. wd400

wd400 said:
one reason to think most of the DNA in the human genome is junk the absence of conservation
Dr JDD

What are you on about? I was answering Barry's question, you seem to be talking about something.... else? wd400

wd400 If you take your head out of the materialist paradigm and a priori commitment to naturalistic evolution with UCD your last statement looks like one "reason" but not a very good one. Take for example all cars ever built. There are certain "conserved" parts. Given you usually always see a steering wheel, if assessing all the cars with no other knowledge of cars you could rightly predict that is probably an important component for functionality, broadly speaking. The mistake to make would to be to then look at a very complex sports car that contains some parts not found in simpler cars and assume they perform no useful or even vital function. Yet there are many complex sports cars that contain essential parts for their functionality that are not found in simpler cars. Just because you do not know the function of that part does not make it functionless. The observation of "conservation" however is entirely consistent with a common designer and reuse of blueprints much like we see shared blueprints for cars. However what would ID predict? It may predict that in more complex organisms we see additional components and functionality to account for the complexity. Evo could predict that too however I think many realise they are in a catch 22 situation if they say that as there are only so many genes neutral drift could account for in the time frames and mutation rates believed be observed. So therefore evos choose to pretend as tho only conserved sequences of DNA actually matter. This approach quite frankly, severely retards scientific progress. Dr JDD

Why would evolutionary conservation necessarily predict functional importance
I don't know about "necessary" but it's certainly true. For instance evolutionary conservation and nothing else (phyloP) is a pretty good predictor of how bad a mutation will be in humans: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003143
After all, we constantly hear that evolution also accounts for vestigial organs and junk DNA (not so much the latter anymore).
Well... yeah... one reason to think most of the DNA in the human genome is junk the absence of conservation.... this is hardly contradictory! wd400

Mr. Arrington as to: "Why would evolutionary conservation necessarily predict functional importance?" It, as you pointed out, doesn't. Evolutionary conservation is a highly misleading way to infer functional importance. In fact, it was by appeal to supposed evolutionary conservation that the Darwinian critics of the ENCODE study, which found widespread functionality for 'junk' DNA, that the Darwinian critics tried to undermine the finding of widespread functionality in the genome:
DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm
So basically, for these Darwinists, functionality did not determine if a sequence is actually functional, only 'conservation of sequence' determined what was functional. In other words, only if Darwinian evolution, (universal common descent), was assumed as true at the outset will Darwinists accept that a given sequence of 'junk' DNA may be functional! That is called 'assuming your conclusion into your premise' and is absolutely horrible science! Apparently some researchers in ENCODE were not so easily intimidated by Darwinists and they fired back with this:
Protracted Unrest Between ENCODE Researchers and Junk-DNA Advocates Goes On - November 26, 2014 Excerpt: In short, the Mouse ENCODE group takes direct aim at the arguments of Dan Graur and the other junk-DNA faithful, who say that everything evolution did not conserve is junk.,,, ,,,much of what Darwinian evolutionists had dismissed as junk appears functional. Non-coding regions of the mouse genome are transcribed, and appear to function in previously unimagined ways, such as regulation of gene expression, chromosomal stability, and maintenance of species identity. http://www.evolutionnews.org/2014/11/protracted_unre091501.html
Of related interest, and completely contrary to evolutionary thought, 'new' ORFan genes, which are definitely not evolutionarily conserved, and many times are found in only one species, are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract
This following study, in which the functional roles of ORFan genes in humans were analyzed, the (Darwinian) researchers were 'very shocked' and 'taken aback' by what they found;
New Genes, New Brain - October 2011 Excerpt: “This is one of the first studies to look at the role of completely novel genes” in primate brain development,,, A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex,,, Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex,,,, “We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.,,, (From the PLoS article, author’s summary: We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events,,, Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination,,) http://the-scientist.com/2011/10/19/new-genes-new-brain/
Needless to say, as the preceding studies highlight, presupposing the functional importance of a sequence in the genome solely through evolutionary conservation is a hindrance to determining true functional importance in the genome. And is, as such, another prime example of Darwinian presuppositions hindering biological science rather than driving it forward. bornagain77

Since first becoming aware of it, I have thought this precludes any notion of 'evolution' involving DNA. End of story. And what if, still another layer in the coding is found? It certainly is just naturally fascinating. butifnot

From the article quoted in the OP:
Additionally, the evolutionary conservation of many of these reading frames suggests functional importance.
Why would evolutionary conservation necessarily predict functional importance? After all, we constantly hear that evolution also accounts for vestigial organs and junk DNA (not so much the latter anymore). Barry Arrington

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