Problems for evolution — squid recodes its own RNA

[noguru]

Have their views changed? See the following: Discovery Institute Condemns Passage of Creationism Bill by Indiana Senate as Bad Science and Bad Education

I think it has evolved into a movement where you just tack "God did it" onto anything in science that is not currently explained entirely through natural processes, rather than remaining strictly a YEC model of "God did it".

:crackup:

I hope y'all caught the strategic use of the word "evolved" there.

 

[6days]

The Discovery Institute may not frequently publish anti-YEC articles as does Biologos, but the DI apparently does actively oppose YE creationism; see this link for example:

http://www.evolutionnews.org/2012/02/discovery_insti_1055841.html

Where you going to with the goal posts? It doesn't matter if anyone publishes anti-YEC material. What I said though is that Biologos publishes anti- christian material. I suggested you look at the thread on that topic. They have had writers all but admit they pose as Christians...and admit their teaching drives people from the church.

 

[Stripe]

:mock: kdhall :loser:

 

[The Barbarian]

Denny wrote, earlier:
Here's just two of the things you 'forgot to include' Professor Stripe:
"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force."

"The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions. (Emphasis added.)"

So the scientists were expecting to find animals like this at some point, the study doesn't discredit evolution in the slightest [It actually credits this new discovery with proving mRNA editing as crucial to evolution in the bold font above], and the study says that both evolution and adaptation (STRIPE BELIEVES IN NEITHER) are supported by "ample evidence."

Congratulations Stripe! You just disproved everything you have been saying on other related threads.

Did you think no one would notice what you deleted, Stipe?

 

[The Barbarian]

How can something be part of a "biblical model" if it isn't in the Bible?

The "biblical model" doesn't have much to do with the Bible.

 

[lucaspa]

Adaptation is a 'piller' of Biblical creation also.

And where is the Biblical justification for that?

6days, "adaptation" is an ad hoc hypothesis to try to save creationism from falsification. Creationists could not deny all the observed examples of adaptation over generations. What they tried to do is say "adaptation within limits" of a "kind".

Problem for evolutionists is they believe in gradual modification. There are numerous examples of rapid change...rapid adaptation. Evidence supports... "In the beginning, God created..."

That is a strawman. First you need to define "gradual". Then you need to define "adaptation".

"Many species once formed never undergo any further change, but become extinct without leaving modified descendants; and the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form." Charles Darwin, Origin of Species, 4th and later editions, pg. 408-409

Notice in this article that the squids are NOT modifying their DNA. Instead, they are modifying the proteins by editing the mRNA. In particular, mRNA is made in exons, and there are proteins that modify which exons, and in which order, are converted to proteins. The proteins that do that are, themselves, coded by DNA. Thus, those proteins have evolved over generations.

 

[lucaspa]

You are getting silly now. Our argument in this thread is that mutations and selection don't, and can't account for the various kinds of animals. Observable science shows how organisms adapt...and often rapidly. *Your belief system requires you to believe in the unobservable.*

What the article showed is that information is processed at mRNA level before it is translated to proteins. Not that big a deal. After all, information is introduced by the folding of the proteins after then come out of the ribosomes. Specific proteins (themselves coded by DNA) called chaperones do this. Also, proteins are glycosylated after synthesis, and in may cases (like proteoglycans), this is essential to their function. Again, the glycosylation is by other proteins, themselves coded by DNA. Some proteins, like HSP90, even determine which isomers of proteins will be transcribed to mRNA. HSP90 is reactive to the environment, but it itself is coded by DNA so it has evolved to do its job.

Now, if mutation and selection cannot account for the diversity of organisms, then there would be independent DNA sequences in different "kinds" of organisms. OTOH, if mutation and selection do account for organisms, their DNA sequences will show patterns of inheritance (from those mutations and selection of an original in the common ancestor). DNA sequences from all organisms -- no matter how diverse -- show a pattern of inheritance.

The vast majority of organisms (with exception *of sponges and possibly Kimberella) in the Ediacaran bear no resemblance to to those in the Cambrian. In other words the pre-cambrian 'animals' like dickinsonia, spriggina and charnia may be plants. They don't have head, gut, sensory organs, *eyes etc.

The Cambrian is the first of mass the radiations following a mass extinction. So most of the Eidacaran organisms went extinct without descendents. The Cambrian organisms arose from different ancestors (soft-bodied). Several of these have been found:

1. http://news.nationalgeographic.com/news/2001/07/0719_crustacean.html Crustacean pre-Cambrian but not hard-shelled.
1a.http://cas.bellarmine.edu/tietjen/Ecology/early_animal_evolution.htm Good summary of radiation from simpler to more complex<BR>
2. Schopf, JW. Solution to Darwin's dilemma: Discovery of the missing Precambrian record of life. PNAS 97: 6947-6953, 2000. http://www.pnas.org/cgi/content/full/97/13/6947
3. Ramskold, L and Hou, 1991 New early Cambrian Animal and Onychophoran
Affinities of Enigmatic Metazoan. Nature, 351: 225-228
4. RA Kerr, Pushing back the origin of animals, Science 279: 803-804, 6 Feb. 1998. The peer reviewed article is C-W Li, J-Y Chen, T-E Hua, Precambrian sponges with cellular structures. Science 279: 879-882. Got embryonic animal fossils that lived 40-50 million years before the Cambrian. Correlates with the molecular data and removes the Cambrian "explosion".
5. Ramskold, L  1992  The second leg row of Hallucigenia discovered. Lethaia, 25: 221-224
6. S Jensen, JG Gehling, MI Droser, Ediacara-type fossils in Cambrian sediments. Nature 393: 567-569, June 11, 1998. Some ediacarans survived into the Cambrian period.
7. HR Vandeberg, Fish tales: pushing back the dawn of the vertebrates. The Sciences 40: 9, Jan/Feb 2000. Describes new fossils from China of fish 530 Mya. First vertebrates. Nov. 4 1999 issue of Nature.
10. RA Kerr, Tracks of billion year old animals? Science 282: 19-20, Oct. 2, 1998. Primary article is  A Selachner, PK Bose, F Pfluger, Triploblastic animals more than 1 billion years ago: trace fossil evidence from India. Science 282: 80-83, Oct. 2, 1998. Shows tracks of worms 200-500 million years before Cambrian.

 

[Stripe]

Denny wrote, earlier: [COLOR="DarkRed"]Here's just two of the things you 'forgot to include' Professor Stripe:"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force.""The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions. (Emphasis added.)"So the scientists were expecting to find animals like this at some point, the study doesn't discredit evolution in the slightest [It actually credits this new discovery with proving mRNA editing as crucial to evolution in the bold font above], and the study says that both evolution and adaptation (STRIPE BELIEVES IN NEITHER) are supported by "ample evidence."Congratulations Stripe! You just disproved everything you have been saying on other related threads.[/COLOR]Did you think no one would notice what you deleted, Stipe?[/QUOTE][QUOTE="The Barbarian, post: 0"]The "biblical model" doesn't have much to do with the Bible.

Until you pick one among "six days" and "billions of years," everything you say can be justifiably ignored, as you haven't a rational leg to stand on when you cannot get the fundamentals right.

And where is the Biblical justification for that?

Evidence, remember? That is what we look at. Organisms can be demonstrated to show adaptation. They cannot be shown to demonstrate evolutionary advance by means of random mutation and selection.

6days, "adaptation" is an ad hoc hypothesis to try to save creationism from falsification. Creationists could not deny all the observed examples of adaptation over generations. What they tried to do is say "adaptation within limits" of a "kind".

Fortunately, that is what we see. :up:

That is a strawman. First you need to define "gradual". Then you need to define "adaptation".

Evolutionists hate dictionaries.

What the article showed is that information is processed at mRNA level before it is translated to proteins. Not that big a deal. After all, information is introduced by the folding of the proteins after then come out of the ribosomes. Specific proteins (themselves coded by DNA) called chaperones do this. Also, proteins are glycosylated after synthesis, and in may cases (like proteoglycans), this is essential to their function. Again, the glycosylation is by other proteins, themselves coded by DNA. Some proteins, like HSP90, even determine which isomers of proteins will be transcribed to mRNA. HSP90 is reactive to the environment, but it itself is coded by DNA so it has evolved to do its job.

You're describing an overall effect in big words to avoid the challenge. How do random mutations and natural selection produce this process you just described?

We have a squid that uses its genetic information to recode its genetic information to suit an environment; completely undermining the theory of evolution.

If mutation and selection cannot account for the diversity of organisms, then there would be independent DNA sequences in different "kinds" of organisms.

There are. lain:

OTOH, if mutation and selection do account for organisms, their DNA sequences will show patterns of inheritance (from those mutations and selection of an original in the common ancestor).

Or similar functions could have been designed similarly.

DNA sequences from all organisms -- no matter how diverse -- show a pattern of inheritance.

Nope. That's your evolutionism speaking. Religious adherence leads to blind faith.

 

[lucaspa]

For anyone interested, you can get the full paper here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384741/

Abstract:
RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

Some important points from the paper that refute the contention that this adaptation did not evolve. First is that it is rare. If God wanted organisms to adapt, why not put this mRNA editing scheme into ALL organisms?

From the Intro:
"DNA sequences were thought to exactly correspond with the sequence of amino acids in the resulting protein. However, it is now known that processes called RNA editing can change the nucleotide sequence of the mRNA molecules after they have been transcribed from the DNA. One such editing process, called A-to-I editing, alters the ‘A’ nucleotide so that the translation machinery reads it as a ‘G’ nucleotide instead. In some—but not all—cases, this event will change, or ‘recode’, the amino acid encoded by this stretch of mRNA, which may change how the protein behaves. This ability to create a range of proteins from a single DNA sequence could help organisms to evolve new traits."

Essentially, this is a another means of mutation. Point mutations do change an A to a G in the DNA; this method does so in the mRNA.

"Alon et al. have now developed a new approach that allows the recoding sites to be identified in organisms whose genomes have not been sequenced. Using this technique—which compares mRNA sequences with the DNA sequence they have been transcribed from—to examine the squid nervous system revealed over 57,000 recoding sites where an ‘A’ nucleotide had been modified to ‘G’ and thereby changed the coded amino acid. "

Basically, the squid uses this method of mutation to generate different variations of about 60% of the squid's proteins.

"Recently, it was suggested that RNA editing is generally not advantageous in humans (Xu and Zhang, 2014), as nonsynonymous events are less frequent than expected by chance (Xu and Zhang, 2014). Strikingly, for sites with high editing levels in squid, the opposite is true (Figure 4B and Figure 4—figure supplement 2A). Recoding events favor creation of glycine and arginine, mainly at the expense of lysine (Figure 4—figure supplement 2B–D). Moreover, highly edited sites within conserved domains tend to recode to amino acids that occur frequently in other species at the same position (Figure 4—figure supplement 3), suggesting selection towards functional substitutions and against deleterious ones."

Oops. Not design, but natural selection.

"An equally intriguing question is why squid edit to this extent? The process clearly creates tremendous protein diversity, and this may in part explain the behavioral sophistication of these complex invertebrates. A recent study showed that editing can be used for temperature adaptation in octopus (Garrett and Rosenthal, 2012b) and this makes sense based on the codon changes that it catalyzes (Garrett and Rosenthal, 2012a) (Figure 4—figure supplement 2C–D). In Drosophila, editing can respond to acute temperature changes (Savva et al., 2012). The large number of sites in squid suggests that editing is well positioned to respond to environmental variation. Most model organisms studied so far are mammals which are homeotherms. Future studies of more diverse species are needed to reveal the extent to which cold-blooded organisms might utilize extensive editing to respond to temperature changes and other environmental variables."

So, as usual the "news article" has overstated the claims. Squids are cold-blooded, but they face a wide variety of water temperatures. Enzymes behave differently at different temperatures. In order to adapt to living in so many different water temperatures, squids have evolved (over millions of years by gradual evolution) this particular system (not extensively used by other species) to generate lots of variations of key proteins. Why? So that some of them will function as the squid moves from cold to warm to cold water again. The proteins have to be in existence all the time, because there is no time to transcribe a different protein in the seconds that the squid moves between water temps. This process has evolved -- by gradual evolution -- in both the ADAR (adenosine deaminase that acts on RNA) enzyme and in the DNA sequence in proteins to provide sites for the ADAR.

Nothing in the paper to challenge evolution, or even the Modern Synthesis. The challenge comes from a distorted news article and the imagination and desperation of creationists.

God created by evolution. Get over it.

 

[User Name]

Religious adherence leads to blind faith.

Is there any other kind? (Hebrews 11:1; Romans 8:24)

 

[Stripe]

God created by evolution. Get over it.

Nope. That's the demands of your evolutionism. When you're prepared to drop the assumption of your religion and address the challenge, let us know. :up:

Is there any other kind?

Yes. Justification.

 

[noguru]

Until you pick one among "six days" and "billions of years," everything you say can be justifiably ignored, as you haven't a rational leg to stand on when you cannot get the fundamentals right.

:rotfl:

The irony is too much sometimes. Stripe giving lessons on "rational legs" is like a wolf giving lesson on having a vegan diet. First, he doesn't understand the difference. And second he does not have the self control to not "wolf down" some rotted meat should the opportunity present itself.

The fundamentals of epistemology do not start with Stripe's proclaimed split of either 6 days or billions of years. I think that YEC's have gotten so use to trying to rewrite science with their nonsensical ideas, it becomes second nature to try and rewrite just about every idea they come in contact with.

 

[User Name]

Yes. Justification.

Justification negates faith?

 

[noguru]

Nope. That's the demands of your evolutionism. When you're prepared to drop the assumption of your religion and address the challenge, let us know. :up:



Yes. Justification.

Taking two "evilustionists" on in one post. You are bad (I mean that in a good way) Stripe. I bet your little cheering section here is real proud of your ability to churn up nonsense.

 

[Stripe]

Justification negates faith?

:AMR:

 

[noguru]

User name is using faith as belief without knowledge. Stripe is using faith more as confidence in his perception of proper scriptural interpretation. User name is more accurately using what society thinks of when "faith" is used. But of course Stripe is again being seduced by a delusion of certainty at the expense of accuracy. And the other YECs love this guy.

:rotfl:

 

[User Name]

User name is using faith as belief without knowledge. Stripe is using faith more as confidence in his perception of proper scriptural interpretation. User name is more accurately using what society thinks of when "faith" is used. But of course Stripe is again being seduced by a delusion of certainty at the expense of accuracy. And the other YECs love this guy.

Stripe attempted to invalidate evolution by alleging that it's "religious adherence leads to blind faith," apparently not remembering that according to his own Bible (Hebrews 11:1), faith is "the evidence of things not seen."

"By faith we understand that the worlds were framed by the word of God, so that the things which are seen were not made of things which are visible." -- Hebrews 11:3​

By faith, not by sight. -- 2 Cor 5:7

 

[Stripe]

Stripe attempted to invalidate evolution by alleging that it's "religious adherence leads to blind faith."

Nope. I issued a specific, scientific challenge. Let's see if you can get on topic. :up:

 

[noguru]

Stripe attempted to invalidate evolution by alleging that it's "religious adherence leads to blind faith," apparently not remembering that according to his own Bible (Hebrews 11:1), faith is "the evidence of things not seen."

"By faith we understand that the worlds were framed by the word of God, so that the things which are seen were not made of things which are visible." -- Hebrews 11:2​

By faith, not by sight. -- 2 Cor 5:7

Stripe likes to play fast and loose with word definitions if it seems to immediately help his argument.

In another thread he is using the same strategy and asking those who accept evolution to suspend their assumption in a basic tenet of the foundation of science. That tenet being "natural processes occur, and we can understand them". He is trying to claim that it is that presupposition which stops those who accept evolution from accepting the YEC model of origins. When in reality it is not that presupposition, because I believe even most YECs accept that "natural processes occur, and we can understand them". In reality it is the YEC additional assumption that "Genesis should be interpreted literally", which is the result of complete and total blind faith, that is added to their set of presuppositions for the foundation of science which leads to their non acceptance of evolution through common ancestry.

 

[lucaspa]

Evidence, remember?

The poster said it was Biblical.

That is what we look at. Organisms can be demonstrated to show adaptation. They cannot be shown to demonstrate evolutionary advance by means of random mutation and selection.

Actually, this is not "evidence", but rather what you think is absence of evidence.

Please define "evolutionary advancement". BTW, "random" simply means "in relation to the needs of the individual or the population". In a climate growing warmer, just as many deer will be born with longer fur as shorter fur. But the shorter fur is advantageous.

What has been shown is that new, beneficial traits have arisen by mutation and selection and that this has led to new species. Here are just a few of, literally, tens of thousands of observations:
1. http://www.lecb.ncifcrf.gov/~toms/paper/ev/
1. David N. Reznick, Mariana Mateos, and Mark S. Springer Independent Origins and Rapid Evolution of the Placenta in the Fish Genus Poeciliopsis Science 298: 1018-1020, Nov. 1, 2002. Intermediate steps in same genus. http://www.u.arizona.edu/~mmateos/reznicketal.pdf News article at: http://www.sciencemag.org/cgi/content/full/298/5595/945a
1. E Wilson-Miles and DR Davies, On the ancestry of barrels. Science 289: 1490. Sept. 1, 2000. "the structure arose from the duplication and fusion of the gene of acommon half-barrel ancestor"
2. M Buck and MK Rosen, Flipping a switch. Science 291: 2329-2330, March 23, 2001. Describes studies on the motion of proteins that are signalling molecules, including mutations that give activity in the absence of phosphorylation. (also refutes Behe because demonstrates one way to build an IC system).
3. http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030139 Formation of gene families and protein folding
4. Science paper by Doolittle (back in 1981) http://www.sciencemag.org/cgi/reprint/214/4517/149.pdf
4. D Normile, How bacterial flagella flip their switch. Science 291: 2065-2066, March 16, 2001. Flagellar filament made up of 11 protofilaments, each formed by stacking tgether numerous molecules of flagellin. Flagellin comes in L and R forms (right and left handed) and each filament is all one or the other form. BUT, one small sequence of amino acids in flagellin will cause entire molecule to flip from R to L under strain. Is how bacteria change direction.
1.Birth of a unique enzyme from an alternative reading frame of the pre-existed, internally repetitious coding sequence", Ohno, S, Proc. Natl Acad. Sci. USA 81:2421-2425, 1984
2. http://www.talkorigins.org/faqs/information/apolipoprotein.html New apo-lipoprotein mutation that adds antioxidant activity.

Fortunately, that is what we see.

You should wait and read all my post first. Later on in the post you found out how wrong you are :doh:.

Evolutionists hate dictionaries.

And what does this have to do with my request to define terms a creationist used? This is a very obvious attempt, Stripe, to avoid providing some definitions.

You're describing an overall effect in big words to avoid the challenge. How do random mutations and natural selection produce this process you just described?

Described in the paper itself and my next post. Mutations in the ADAR to make it more active (including a more active isoform) and mutations in the DNA to make an A so the ADAR can work on it.

We have a squid that uses its genetic information to recode its genetic information to suit an environment; completely undermining the theory of evolution.

First, the squid is NOT "recode its genetic information" in that it is not changing its DNA. There are point mutations in the mRNA. Second, it is not doing so to "suit an evironment". That is, the squid doesn't swim from 4° C water to 15° C water and then starts making the new variant of the protein that fits the warmer water better.

Let me try to simplify this for everyone:
The squids are making the mRNA for their proteins. We'll just look at a hypothetical one -- call it protein A.

The squid is constantly transcribing protein A. That is, it is copying the DNA sequence to an mRNA -- mRNA(A). (The mRNA will be translated to a protein.) The squid is also making an enzyme called ADAR. This enzyme can change an adenosine (A) on the mRNA to a guanine (G). Because amino acids are a codon of 3 nucleotides, depending on which A is changed to G, you could get a different amino acid, and thus a variation in that protein.

Some molecules of mRNA(A) do not get changed. They make protein A. Some molecules of mRNA(A) have one A changed to G. That gives protein A1. Some molecules of mRNA(A) have 2 different As changed to G. That produces protein A2. So, for a single DNA sequence, the squid produces 3 proteins: A, A1, A2. ALL of them are present all the time.

However, because A, A1, and A2 are different, they behave slightly differently. Most of the changes have to do with how the proteins behave in different temperatures. A works better at 4°C, A1 works best at 10°C, and A2 works best at 20° C.

While the squid is in 4°C water, A is doing the job most efficiently. When the squid swims into 10°C water, then A1 will take over the function. Move to 20°C water, and now A2 takes over the function.

So, by having ALL THREE variations at the same time, the squid is ready no matter what the water temperature is.

Now you see where the gradual evolution comes into play. Not only is there gradual change in ADAR enzyme to do more changing, there are also gradual changes in the DNA of protein A to make sites for the ADAR to work on, and selection so that the sites, when changed, actually make a protein that works under the circumstances.

There are.

No, there are not. Phylogenetic analyses of DNA sequences have shown sequences from different organisms are related through historical connections.
1. http://www.biotechniques.com/news/T...0_5f518744d7-b8e81141ff-87692357#.VMjkRdJ4qhU
2. DM Hillis, Biology recapitulates phylogeny, Science (11 April) 276: 276-277, 1997.

Or similar functions could have been designed similarly.

It doesn't work that way. Think of car companies. They design similarly for similar functions, but cars are not related through historical connections -- particularly between major "kinds" (companies). Living organisms have DNA sequences that are.

Nope. That's your evolutionism speaking. Religious adherence leads to blind faith.

See references above. As you said, evidence. Your belief in the lack of such evidence is your adherence to a blind faith.