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.
From the article quoted in the OP:
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).
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.
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:
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:
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:
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;
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.
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/plosg.....en.1003143
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 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.
What are you on about? I was answering Barry’s question, you seem to be talking about something…. else?
wd400 said:
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.
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.
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.
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.
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.
Barry
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.
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:
etc.. etc.. etc..
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:
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:
Dr JDD,
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.
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.
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.
How come when I read one of your posts Popperian I am reminded of this quip from Berlinski?
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:
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
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…
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.
wd400,
Bornagain77 mentioned it in 3. Here’s the link so you won’t have to scroll up:
http://www.sciencedaily.com/re.....142523.htm
I was astounded, but I assumed that you wouldn’t be.
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
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.
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.
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/.....areer2.jpg
As I quoted earlier,
‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’
Berlinski
BA77 #25,
Very good choice of illustration for Popperian’s style 🙂
wd400 stated this
in regards to this comment by Querius:
Which Querius stated in regards to this observation,,
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.
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.
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!
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:
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
Very interesting article. Thank you.
Here’s a relatively recent paper that might serve as illustration for some of the ongoing discussions:
http://www.uncommondescent.com.....ent-566910
Dr JDD @28,
I’m sitting front row on this one. BTW I’m wondering how much AltORFs we humans share with chimpanzee/bonobo.
Dr JDD
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. 🙂
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.
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, 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.
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.
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.
Dr DD wrote:
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?
Mung:
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.
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.
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
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.
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.
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.
wd400 at 41 claims
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:
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:
The authors also comment in the main paper:
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:
You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:
Multicellular creatures have the same ‘anomaly’ of unexpectedly large percentage of new ORFan genes found in each new species sequenced:
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:
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:
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 JJ:
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.
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.
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/2.....64291.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/re.....133930.htm
Wd400 said,
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.
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.
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.
The irony has been noted. 😉
-Q
I don’t know Q, this sounds like someone claiming something about conservation to me…
It’s also just wrong. (It’s not the only way to infer function, but no one has claimed that to be the case)
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.
Popperian complained,
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.
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.
Isn’t evolution dependent on competition as well? 😮
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
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/.....egnor.html
Dr JDD
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.
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.
Still with me? If not, where does your view differ and how?
wd400 retreated with,
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
wd400:
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.
“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!
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.
No.
Note that none of this suggests to wd400 that Darwinism could possibly be false!
Dr JDD:
Actually wd400 is right. They are inefficient. But that’s hardly a point in itself. Evolutionary theory needs to explain why.
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?
bornagain77 quoted,
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
Inefficient? Inefficient by whose standards?
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):
As well the cell is found to be optimal in its metabolic efficiency:
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:
ditto for photosynthesis:
wd400 admitted,
How does subfunctionalization relate to the following?
http://www.sciencemag.org/cont.....9.abstract
-Q
It does not.
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
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,
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.
Mung:
Steel ICEs operate at 18 %-20 % efficiency on average.
From Wikipedia:
So, they operate at an average of 85% of maximum possible efficiency.
Mung:
Wikipedia:
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?
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…
Dr JDD:
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
Another example?
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.
Dr JDD:
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.
A few notes on the overlapping complexity in DNA
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.
Popperian:
LoL LoL Muwahaha LoL LoL Muwahaha Muwahaha
Moron. [Someone had to say it.]
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).
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 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.
Popperian, to answer now your second point (which did not answer my question but jumped straight over it):
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: 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.
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:
http://www.uncommondescent.com.....ent-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?
Dr JDD
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.
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.
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.
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 @ 78 asserted,
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