Original Research--join In

[Loudmouth]

I totally agree... however, we would need to be examining the genomes right after the original creation, not thousands or more years afterwards. Evolution has added way too much confusing stuff since then. And who says that genetic recombination would not be the intent of the designer--a designer who loves diversity--a designer who knows the value of variation and adaptation? Quit making a straw man of the design/creation paradigm.

A designer could give a whale species and humans the exact same gene sequence for cytochrome C while giving an ape species (e.g. orangutan) a cytochrome C gene that differed from whales and humans by 20%. There is nothing stopping a designer from doing so.

So how would evolution make orangutan and human cytochrome C nearly 100% identical over a few thousand years? How would the unguided processes of evolution know which bases to mutate in both orangutans and humans to make them more similar? Evolution can't do that. The only expectation is that evolution will cause all sequences to diverge over time. For the mock example above, if evolution adds another 5% of divergence then the difference between the whale and humans will be 5% and 25% difference between orangutans and humans. Humans and orangutans will not become more similar over time while whales and humans become less similar. That isn't how evolution works.

Therefore, the nested hierarchy had to be there from the very start. It couldn't have developed after the species were already created. Evolution can not mask clear and obvious violations of a nested hierarchy that a designer could so easily produce.

 

[WisdomSpy]

Loudmouth posted: “My position is that the observed similarities and the pattern that the similarities fall into are all consistent with what we would expect from evolution. That is why these observations are evidence for evolution.”

No, your observations are only proof of your observations. The conclusions you arrive at while pondering your observations are evidence only that your expectations have become a self-fulfilling prophecy, not because the evidence proves it but because your story-telling about your observations does, in your mind. It’s called circular reasoning—one of the classic errors of logic. If you keep expecting your story-telling to be true, and allowing for no other, you will continue to concoct ever-so complex stories which distract you from the fact that you have failed to exercise critical thinking. Mythology is great entertainment but lousy science. At some point, you need to face the music and deal honestly with demonstrable and repeatable science involving cell biochemistry and the math.

Examine the genome of the microsporidia Encephalitozoon cuniculi or intestinalis and show us a model which credibly explains how undirected processes could have turned one into the other, or generated either from a common ancestor. Hint: you are going to need to deal with the natural results of undirected insertions, deletions, splicing events, etc. of lengthy sequences of DNA. BTW, can you show that anything like this happened during Lenski's observed 50,000 generations of E. coli subjected to completely un-natural selection pressure?

 

[Loudmouth]

Every casino on earth is hoping you will come play their games! You, like so many evolutionists are failing to apply the law of averages. Why don't you do something original and spend time with the online random DNA sequence generator. See how long it takes you to generate a 100 codon sequence (300 nucleotides) which fortuitously lacks internal stop codons.

Thought I would give this a try, just for kicks. It only took one try. Here is the random sequence generator. I used the default settings for a 1kb sequence and 50% GC content.

Random DNA Generator

This is the sequence:

GTCGACCAAGAACCGCTAGATGCGTCGCTGTACAAATAGTTGTCGACAGA
CCGTCGAGTTTAGAAAATGGTACCAGCATTTTCGGGGGATCTCAATCAAG
TATGGATTACGGTGTTTACACTGTCCTGCGGCTACCCATGGCCTGAAATC
CAGCTCGTGTCAAGCCATTGCCTCTCCGGGACGCCGCATGAAGTAATACA
TATACCTTGCACGGGTTCACTGCGGTCCGTTCAGAGTCGACCAAGGACAC
AATCGAGCTCCGATCCGTATGCTCGACTAACTTGTACCCAACCCCCGGAG
CTTGGCAGCTCCTGGGGTATCATGGAGCCTGTGGTTCATCCCGTCGGATA
TCAAACTTCGTCTTGATAAAGCCCCCCGCTCGGGAGTACCAGAGAAGATG
TCTACTGAGTTGTGCGATCCCTGCACTTCAGCTAAGGAAGCTACCAATAT
TTAGTTTCTGAGTCTCACGACAGACCTCGCGCGTAGATTGCCATGCGTAG
AGCTAACGAGCCAGCGGAAAGCGTGAGGCGCTTTTAAGCATGGCGAGTAA
GTGATCCAACGCTTCGGATATGACTATATACTTAGGTTCGATCTCGTCCC
GAGAATTCTAAGCCTCAACATCTATGAGTTATGAGGTTAGCCGAAAAAGC
ACGTGGTGGCGCCCACCGACTGTTCCCAGACTGTAGCTCTTTGTTCTGTC
AAGGCCCGACCTTCATCGCGGCCGATTCCTTCTGCGGACCATACCGTCCT
GATACTTTGGTCATGTTTCCGTTGTAGGAGTGAACCCACTTGCCTTTGCG
TCTTAATACCAATGAAAAACCTATGCACTTTGTACAGGGTACCATCGGGA
TTCTGAACCCTCAGATAGTGGGGATCCCGGGTATAGACCTTTATCTGCGG
TCCAACTTAGGCATAAACCTCCATGCTACCTTGTCAGACCCACCCTGCAC
GAGGTAAATATGGGACGCGTCCGACCTGGCTCCTGGCGTTCTACGCCGCC

Plugged it into ORF finder

ORF Finder

There is a 300 bp open reading frame for a 99 aa protein. Go figure.

Added in edit: if you increase the random genome to 10,000 bases (10kb), you can get 300 base open reading frames with ease. Bacterial genomes are usually over 2 million bases, and vertebrate genomes are usually over 2 billion. The type of open reading frames that WS is asking for a quite easy to produce in these conditions.

 

[Loudmouth]

No, your observations are only proof of your observations. The conclusions you arrive at while pondering your observations are evidence only that your expectations have become a self-fulfilling prophecy, not because the evidence proves it but because your story-telling about your observations does, in your mind.

How do my "self fulfilling prophecies" cause human and chimp genes to share ~99% identity while human and mouse genes share much less identity? Do I have paranormal abilities that allow me to change DNA sequences with the power of my mind?

Examine the genome of the microsporidia Encephalitozoon cuniculi or intestinalis and show us a model which credibly explains how undirected processes could have turned one into the other, or generated either from a common ancestor. Hint: you are going to need to deal with the natural results of undirected insertions, deletions, splicing events, etc. of lengthy sequences of DNA. BTW, can you show that anything like this happened during Lenski's observed 50,000 generations of E. coli subjected to completely un-natural selection pressure?

It seems that you still don't understand the evidence I am presenting to you.

Do you understand what a nested hierarchy is?

29+ Evidences for Macroevolution: Part 1

 

[WisdomSpy]

Originally Posted by WisdomSpy View Post
A thousand base substitutions can NEVER turn the hemoglobin gene into the Dystrophin gene.

Loudmouth's reply: I wasn't aware that anyone was claiming that it could, or that the dystrophin gene evolved from an ancestral hemoglobin gene.

You are dodging the point--it was an example of the hypothesis inherent to evolution theory that short genes could become or give rise to long genes, as a result of mutations. My experiments which are applicable to abiogenesis, as well as evolution downstream of that, indicate that Neo-Darwinian ideas about this are purely mythology. A reasonable step-by-step analysis of the hypothetical events, combined with an accounting of the molecular resources needed ahead of time and then produced afterwards, reveals the secret to origins.

 

[Loudmouth]

You are dodging the point--it was an example of the hypothesis inherent to evolution theory that short genes could become or give rise to long genes, as a result of mutations.

Are you denying that genetic recombination occurs?

My experiments which are applicable to abiogenesis, . . .

They aren't applicable to abiogenesis since the first life may not have even had DNA or 3 base codons. I have explained this before.

 

[WisdomSpy]

Loudmouth, thank-you for finally doing the original research I suggested--posting your results from the random DNA sequence generator. Unfortunately, you did not follow through by separating the sequence into nucleotide triplets so that you could identify the stop codons. As it turns out, the 13th codon in your sequence is a stop codon:
GTC GAC CAA GAA CCG CTA GAT GCG TCG CTG TAC AAA TAG

Hence, this sequence CANNOT produce an amino acid chain of 99, or anything close to it. Now, before going on with further trials (which I hope you do), you must realize that applying this to actual chemistry means that this chain you generated has linked up these molecules for perhaps millions of years. You cannot simply re-shuffle them like cards. Resources MUST be accounted for in the modeling of origins.

Continue the trials until you find a sequence of 100 codons without internal stops, then tell me how many molecules were used up.

There is a straight forward calculation which can tell you the number, on average, that would be needed for this task. Any guesses as to the proper equation? Hint: it's not linear, it's exponential.

 

[WisdomSpy]

Loudmouth posted: "They aren't applicable to abiogenesis since the first life may not have even had DNA or 3 base codons."

You realize, I hope, that you are story-telling again, with no scientific evidence to back it up. Reproducible information transmittal requires set recognizable beginnings and endings. No matter if you hypothesize that RNA or proteins (or elf-atoms or Santa-molecules) were the initial bearers of information, you must recognize the absolute requirement for start and stop signals. The math does not get any easier with any hypothetical substitutes for DNA.

In case you are tempted to post something regarding the supposed "self-replicating RNA", I suggest you read the actual articles and diligently separate fact from fiction. The fact that these articles were even "peer reviewed" and published is a testament to the bias which exists today in favor of the evolutionary paradigm, no matter how utterly contorted the data actually is. It's really on a par with Piltdown, you know.

 

[Loudmouth]

Loudmouth, thank-you for finally doing the original research I suggested--posting your results from the random DNA sequence generator. Unfortunately, you did not follow through by separating the sequence into nucleotide triplets so that you could identify the stop codons. As it turns out, the 13th codon in your sequence is a stop codon:
GTC GAC CAA GAA CCG CTA GAT GCG TCG CTG TAC AAA TAG

Hence, this sequence CANNOT produce an amino acid chain of 99, or anything close to it.

There are 6 frames to look at, 3 on the positive strand and 3 on the negative strand. You only looked at one frame, and you didn't even go further in than 100 bases into the 1,000 base sequence. Didn't you plug the sequence into ORF Finder like I did?

ORF Finder

Just so you understand, here is a sample sequence and the 3 frames on the positive strand:

sequence: AAAGGGCCCTTTGGGAAACCCGGG

frame 1: AAA GGG CCC TTT GGG AAA CCC GGG
frame 2: A AAG GGC CCT TTG GGA AAC CCG GG
frame 3: AA AGG GCC CTT TGG GAA ACC CGG G

For the negative strand, get the reverse complement here (DNA is double stranded, don't forget):

Reverse complement

reverse complement: CCCGGGTTTCCCAAAGGGCCCTTT

and then do the same as above for this sequence. 6 frames in all, 3 on the positive strand and 3 on the negative strand.

Now, before going on with further trials (which I hope you do), you must realize that applying this to actual chemistry means that this chain you generated has linked up these molecules for perhaps millions of years. You cannot simply re-shuffle them like cards. Resources MUST be accounted for in the modeling of origins.

Again, are we talking about abiogenesis or evolution? You need to pick one.

Continue the trials until you find a sequence of 100 codons without internal stops, then tell me how many molecules were used up.

I got 100 codon open reading frame on the very first try in a 1,000 base genome. Plug it into ORF Finder yourself if you don't believe me. I got 3 for a 10,000 base genome.

 

[Loudmouth]

You realize, I hope, that you are story-telling again, with no scientific evidence to back it up.

You have no scientific evidence that the first life had DNA. You are the one telling stories.

Reproducible information transmittal requires set recognizable beginnings and endings.

Have you heard of RNA enzymes?

No matter if you hypothesize that RNA or proteins (or elf-atoms or Santa-molecules) were the initial bearers of information, you must recognize the absolute requirement for start and stop signals.

What evidence do you have that the first life used 3 base codons and the same stop and start codons? Perhaps you should start there. Show us the genome of the first organism.

 

[Loudmouth]

Just so WS understands that I am not making this up, I have highlighted the 300 bp open reading frame in the context of the original random sequence, in red from start to stop codon:

GTCGACCAAGAACCGCTAGATGCGTCGCTGTACAAATAGTTGTCGACAGA
CCGTCGAGTTTAGAAAATGGTACCAGCATTTTCGGGGGATCTCAATCAAG
TATGGATTACGGTGTTTACACTGTCCTGCGGCTACCCATGGCCTGAAATC
CAGCTCGTGTCAAGCCATTGCCTCTCCGGGACGCCGCATGAAGTAATACA
TATACCTTGCACGGGTTCACTGCGGTCCGTTCAGAGTCGACCAAGGACAC
AATCGAGCTCCGATCCGTATGCTCGACTAACTTGTACCCAACCCCCGGAG
CTTGGCAGCTCCTGGGGTATCATGGAGCCTGTGGTTCATCCCGTCGGATA
TCAAACTTCGTCTTGATAAAGCCCCCCGCTCGGGAGTACCAGAGAAGATG
TCTACTGAGTTGTGCGATCCCTGCACTTCAGCTAAGGAAGCTACCAATAT
TTAGTTTCTGAGTCTCACGACAGACCTCGCGCGTAGATTGCCATGCGTAG
AGCTAACGAGCCAGCGGAAAGCGTGAGGCGCTTTTAAGCATGGCGAGTAA
GTGATCCAACGCTTCGGATATGACTATATACTTAGGTTCGATCTCGTCCC
GAGAATTCTAAGCCTCAACATCTATGAGTTATGAGGTTAGCCGAAAAAGC
ACGTGGTGGCGCCCACCGACTGTTCCCAGACTGTAGCTCTTTGTTCTGTC
AAGGCCCGACCTTCATCGCGGCCGATTCCTTCTGCGGACCATACCGTCCT
GATACTTTGGTCATGTTTCCGTTGTAGGAGTGAACCCACTTGCCTTTGCG
TCTTAATACCAATGAAAAACCTATGCACTTTGTACAGGGTACCATCGGGA
TTCTGAACCCTCAGATAGTGGGGATCCCGGGTATAGACCTTTATCTGCGG
TCCAACTTAGGCATAAACCTCCATGCTACCTTGTCAGACCCACCCTGCAC
GAGGTAAATATGGGACGCGTCCGACCTGGCTCCTGGCGTTCTACGCCGCC

 

[sfs]

I got 100 codon open reading frame on the very first try in a 1,000 base genome. Plug it into ORF Finder yourself if you don't believe me. I got 3 for a 10,000 base genome.

That's pretty funny. You'd better rush to publish your research . . .

 

[Loudmouth]

That's pretty funny. You'd better rush to publish your research . . .

The funny part was that I honestly got a 300 bp ORF on the very first try, the exact number that WS was asking for.

Hopefully, WS can walk away with a better appreciation for how open reading frames work and how they are found.

 

[bhsmte]

I have a hunch we have one person posting under 2 handles in this thread.

 

[WisdomSpy]

Loudmouth posted: "The funny part was that I honestly got a 300 bp ORF on the very first try, the exact number that WS was asking for."

You keep neglecting to follow through and answer my underlying question. I never said you could not come up with a sequence of 100. That would be ridiculous. I asked how many molecules would be tied-up uselessly ON AVERAGE, for each success? You haven't done the math yet.

Decide how many information units ("genes" or whatever you want to call them) that you believe might have been in the first hypothetical "protocell". It's pretty clear from existing genomic data that the number would be around 1500 to 2000 in order to confer sufficient metabolic and reproductive capacities. And, as posted by someone earlier, those genes have an average length well over 1500 bp long.

Now, be responsible and run the math. Count up the number of nucleotides bound up in useless sequences and then ask yourself if such a "cell" or "protocell" is likely to function. Is the amount of junk in it commensurate with any known living cell?

I would remind you also that we have been doing the most rudimentary analysis. In essence, you are assuming that each of the "successes" in producing a sequence free of stops also just happens to contain an appropriate combination of codons to create a functional polypeptide molecule. Do you realize how utterly presumptuous that is?

 

[Loudmouth]

Loudmouth posted: "The funny part was that I honestly got a 300 bp ORF on the very first try, the exact number that WS was asking for."

You keep neglecting to follow through and answer my underlying question. I never said you could not come up with a sequence of 100. That would be ridiculous. I asked how many molecules would be tied-up uselessly ON AVERAGE, for each success? You haven't done the math yet.

That sound you hear is the goalposts scraping along the ground as you move them about the field.

"Every casino on earth is hoping you will come play their games! You, like so many evolutionists are failing to apply the law of averages. Why don't you do something original and spend time with the online random DNA sequence generator. See how long it takes you to generate a 100 codon sequence (300 nucleotides) which fortuitously lacks internal stop codons."

It took me less than 5 seconds to do what you claimed would be so difficult. I did it with just 1,000 bases of random sequence, and on the first try to boot.

300 bases in a 1,000 base genome is better than the human genome which has less than 3% of its bases tied up in codons. In fact, at 3% or so fo a 3 billion base genome, the human genome is much more effecient than some other genomes. The onion genome has 100 billion bases, 30 times the human genome. There is a species of amoeba that has a genome of over 600 billion bases.

Decide how many information units ("genes" or whatever you want to call them) that you believe might have been in the first hypothetical "protocell". It's pretty clear from existing genomic data that the number would be around 1500 to 2000 in order to confer sufficient metabolic and reproductive capacities.

Please, show us this genomic data. You have everything wrong so far . . . let's see how far the rabbit hole goes.

The irony here is that you didn't even understand how to find open reading frames in sequence. I bet you didn't even consider the reverse complement for the negative strand.

Now you want to tell an entire field of scientists that they are all wrong, and you are right. I think you can understand our skepticism.

Now, be responsible and run the math. Count up the number of nucleotides bound up in useless sequences and then ask yourself if such a "cell" or "protocell" is likely to function. Is the amount of junk in it commensurate with any known living cell?

Yep, sure is.

I would remind you also that we have been doing the most rudimentary analysis. In essence, you are assuming that each of the "successes" in producing a sequence free of stops also just happens to contain an appropriate combination of codons to create a functional polypeptide molecule. Do you realize how utterly presumptuous that is?

I realize the presumptuousness, but it isn't on my side of the conversation.

 

[Loudmouth]

There are some other interesting aspects to this discussion that are worth pursuing. If we inserted some random sequence into a gene, could that random sequence evolve function? The answer is yes.

J Mol Evol. 2003 Feb;56(2):162-8.

Can an arbitrary sequence evolve towards acquiring a biological function?

Hayashi Y1, Sakata H, Makino Y, Urabe I, Yomo T.

To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.
Can an arbitrary sequence evolve towards acquiring a biological fun... - PubMed - NCBI
​

They disrupted the function of a gene with random sequence, but through mutation and selection (i.e. evolution) the gene regained function. In fact, that new function was entirely dependent on the evolved random sequence. Not only was the newly evolved phage infective, it was over 200 times more infective than the wild type that does not have the evolved random sequence.

 

[Loudmouth]

Since WS seems to be focoused on abiogenesis as well, it might be worth asking if random RNA molecules can have function. Can a random sequence of nucleotides produce a functioning RNA enzyme? As it turns out, yes they can.

Science. 1995 Jul 21;269(5222):364-70.

Structurally complex and highly active RNA ligases derived from random RNA sequences.

Ekland EH1, Szostak JW, Bartel DP.


Seven families of RNA ligases, previously isolated from random RNA sequences, fall into three classes on the basis of secondary structure and regiospecificity of ligation. Two of the three classes of ribozymes have been engineered to act as true enzymes, catalyzing the multiple-turnover transformation of substrates into products. The most complex of these ribozymes has a minimal catalytic domain of 93 nucleotides. An optimized version of this ribozyme has a kcat exceeding one per second, a value far greater than that of most natural RNA catalysts and approaching that of comparable protein enzymes. The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity.
Structurally complex and highly active RNA ligases derived from ran... - PubMed - NCBI
​

They have found RNA ligases from random sequences of RNA. No DNA, protein, or codons needed.

 

[Loudmouth]

RNA enzymes are actually kind of cool, so here is another article. Yet another random RNA sequence that produces an RNA enzyme that carries the same genetic information found in very real genomes.

Proc Natl Acad Sci U S A. Jan 5, 1999; 96(1): 173–178.

PMCID: PMC15112

Evolution

Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution

Laura F. Landweber* and Irina D. Pokrovskaya

In vitro selection, or directed molecular evolution, allows the isolation and amplification of rare sequences that satisfy a functional-selection criterion. This technique can be used to isolate novel ribozymes (RNA enzymes) from large pools of random sequences. We used in vitro evolution to select a ribozyme that catalyzes a novel template-directed RNA ligation that requires surprisingly few nucleotides for catalytic activity. With the exception of two nucleotides, most of the ribozyme contributes to a template, suggesting that it is a general prebiotic ligase. More surprisingly, the catalytic core built from randomized sequences actually contains a 7-nt manganese-dependent self-cleavage motif originally discovered in the Tetrahymena group I intron. Further experiments revealed that we have selected a dual-catalytic RNA from random sequences: the RNA promotes both cleavage at one site and ligation at another site, suggesting two conformations surrounding at least one divalent metal ion-binding site. Together, these results imply that similar catalytic RNA motifs can arise under fairly simple conditions and that multiple catalytic structures, including bifunctional ligases, can evolve from very small preexisting parts. By breaking apart and joining different RNA strands, such ribozymes could have led to the production of longer and more complex RNA polymers in prebiotic evolution.
Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution
​

 

[JacksBratt]

When it comes to science, christians have been at the buffet since Galileo. Why stop now? Or are you a Geocentrist as scripture demands?

I am certainly not a Geocentrist. Please show me scripture that states that the earth is the center of the universe.