Message 212 of 373 (646472) 01-04-2012 6:38 PM

Reply to: Message 210 by Taq 01-04-2012 5:20 PM

Cytochrome C is used by almost all organisms. I would say that several other proteins/enzymes are almost universal. If every little biochemical reaction that takes place in a cell requires transcription and translation, an enormous amount of dna would be needed and would likely be unable to be stored and utilized in an efficient manner if every biochemical reaction corresponded to a single exact sequence of DNA. It would be much more effective , for example, if you designed some of these enzymes/proteins to function the same under numerous different amino acid sequences. Doing so would allow you to use the corresponding gene for purposes other than transcribing the RNA necessary for that particular enzyme/protein. That same gene could be transcribed with other genes, and then spliced thousands of different ways to produce thousands of different miRNAs.

The tuna, pidgeon, horse, drosophila fly, rat and yeast all have different biochemical pathways from each other, and yet all of these pathways use cytochrome C at some time or another. Why not design cytochrome C in such a way that it can perform the same function in a myriad of amino acid sequences? If every animal listed above had a cytochrome C protein that would only function with a specific amino acid sequence, the corresponding gene would likely only produce cytochrome C, and be less likely to be used for other regulatory functions. This would be because you would not be able to put other sequences in it that could serve other functions. If you did, you would destroy the function the gene was mainly designed for.

To summarize: cytochrome C from one organism fits in to the cellular machinery of many other organisms in order to cut down on DNA storage space. One to one correspondence of gene to protein product is wasteful and inefficient.

Message 213 of 373 (646473) 01-04-2012 6:44 PM

Reply to: Message 210 by Taq 01-04-2012 5:20 PM

Nested hierarchies are manmade inventions. Cytochrome C was not designed to make it look like evolution occurred. Men see evolution when there is none. That isn't God's fault. You are going to have to show me how cytC produces nested hierarchies and how morphologies produce nested hierarchies before I can decide if they do indeed look the same, and if so, what reason would be behind it.

Message 215 of 373 (646476) 01-04-2012 6:57 PM

Reply to: Message 214 by Trixie 01-04-2012 6:48 PM

I didn't say any other proteins would be produced. I said micro RNAs would be produced. These micro RNAs are known to have regulatory function, mainly transcription regulation. As you know, which genes are transcribed and which ones are not, at any one time, make an enormous difference in cellular chemistry.

Message 216 of 373 (646482) 01-04-2012 7:16 PM

Reply to: Message 215 by foreveryoung 01-04-2012 6:57 PM

What do you mean by this?

Message 217 of 373 (646487) 01-04-2012 7:30 PM

Reply to: Message 216 by Trixie 01-04-2012 7:16 PM

What determines when a gene gets transcribed and when it is turned off is partly determined by micro RNAs. If you had a seperate gene devoted to turning on and off another single gene for all the genes in a human, more DNA space would be required.

In short, a one to one gene to gene product correspondence would require an enormous amount of DNA space. Doing more transcription work in less space is efficient. Not doing so is inefficient.

Message 218 of 373 (646502) 01-04-2012 8:51 PM

Reply to: Message 212 by foreveryoung 01-04-2012 6:38 PM

Well no, since all the organisms you listed are eukaryotes they all use cytochrome C in exactly the same biochemical pathway i.e. in the electron transport chain following the Kreb's cycle. Since they are involved in an essential pathway they should be highly conserved, yet as others have pointed out we see the genes have acquired mutations in a pattern that conforms to the ToE's predicted nested hierarchy.

Your argument seems to be that the difference is a result of alternative splicing to get different proteins or RNA interference. However, the alternative splicing arises from the excision of introns from transcribed mRNA and this can give rise to multiple proteins from a single gene. However none of the cytochrome C subunit genes have introns so this would not be an issue. As for RNA interference, as far as I'm aware such sequences in the genome would not give rise to functional proteins, and besides this would only affect how genes are expressed, not their sequence, although I could be wrong as it's a bit beyond what I learned at uni.
I'd also question that this was all an effort to make reduce the DNA required for the storage of protein coding sequences, given that half our genome is repetitive retrotransposon sequences.

Edited by Malcolm, : No reason given.

Message 219 of 373 (646503) 01-04-2012 8:58 PM

Reply to: Message 213 by foreveryoung 01-04-2012 6:44 PM

The tree below is drawn from Cytochrome C differences. The lengths of the branches and twigs correspond to the numbers of differences. Do you see the point that it comes out very similar to what would be expected from morphology?

The point about Cytochrome C is that the differences are irrelevant to function, so there's no need for this resemblance.

So, what reason is there behind this, and, in relation to the O.P., what would we expect to see in a designed world?

Message 220 of 373 (646547) 01-05-2012 6:17 AM

Reply to: Message 215 by foreveryoung 01-04-2012 6:57 PM

OK, so what microRNAs are associated with the Cytochrome C gene sequence? Certainly microRNA exist and have regulatory functions, but what evidence is there that there is any association of microRNAs produced from Cytochrome C sequences in different species with different regulatory networks? This seem to be a pretty specific claim, is there actually any research that would support it or are you just making up ad hoc explanations with a trendy hot topic term thrown in?

It seems a particularly specious argument that this is some sort of highly efficient system compressing more functions into one sequence when there are about 50 pseudogene forms of Cytochrome C in the human genome.

So where are all these examples of protein coding gene sequences which also encode multiple functional microRNAs?

I am certainly aware of some examples of dual function microRNAs which both act as mediators of gene regulation in their RNA form and as templates for proteins ( Wadler and Vanderpool, 2007; Gimpel et al., 2010; Vanderpool et al., 2011), but these come nowhere near the extent you are suggesting and are all from bacteria.

There are some examples in the eukaryotes of RNAs from coding sequences which fulfill functional roles other than as templates for protein synthesis, but these roles are not as microRNAs (Ulvelling et al., 2011). I am certainly onboard with the idea that other layers of information, regulatory and structural amongst others, can be encoded overlapping with protein coding sequences (Itzkovitz et al., 2010 PDF) and there are even instances of overlapping protein coding sequences, but I am unaware of the situation you suggest being a common one, as it would need to be for your explanation of the diversity of homologous genes to make sense.

TTFN,

WK

Edited by Wounded King, : added some spacing

Message 221 of 373 (646570) 01-05-2012 11:16 AM

Reply to: Message 213 by foreveryoung 01-04-2012 6:44 PM

Bluegenes has already addressed this in Message 219, and we can get into the evidence for nested hierarchies in more detail if you like, but I'm trying to see the "Evidence to expect given a designer" in your argument and can't find it. Your argument appears similar to the same arguments others offered earlier, namely that whatever we find, that's what God did.

As others have pointed out, if the genomes of species were designed then we should expect to find many examples of genes with no similarity to genes in other species. At the morphological level we should expect to find characteristics crossing family, order and class boundaries, e.g., ostriches with hooves, seals with bills, whales with gills, squirrels with wings, and so forth.

I suppose one way to approach the discussion is just to look at the existing evidence and claim that it is better explained by God than by nature, but it's hard to imagine anything that couldn't be explained by God. I think you need evidence of things that can't be explained by evolution. The claim that evolution can't explain the diversity of life both extant and in the fossil record has no support and is just an argument from incredulity, while the fact that species change over time is an inevitable consequence of the imperfect copying that takes place during the process of reproduction we already know so much about. All evidence we find is consistent with an evolutionary view of life, from cosmology to astronomy to geology to paleontology to biology.

Lack of a nested hierarchy of life would be as much evidence for design as a the presence of this hierarchy is for evolution, but that's been obvious to everyone on the evolution side for decades. If life that didn't fit a nested hierarchy were found it would be big news and we'd all know about it already if it existed.

There wouldn't be much point to arguing about whether life, both at the morphological and genetic levels, fits within a nested hierarchy. You could deny this fact, just refuse to accept it, and I for one would just let you go your own way because you won't make much headway anywhere with a head-in-the-sand approach.

It would be much more interesting if someone on the creationist side could describe the type of evidence we should see were there a designer and that isn't just a misinterpretation of evidence we already have.

--Percy

Message 222 of 373 (646574) 01-05-2012 11:39 AM

Reply to: Message 212 by foreveryoung 01-04-2012 6:38 PM

Is it though? I guess it depends on how you look at it. We humans use the same name for these enzymes in various species because they have the same function and evolutionary ancestry. Without homology based on evolutionary history, why should we use the same name for each of these enzymes? Their sequence differs greatly between distantly related . . . err, I mean different organisms.

"It has been shown that the human cytochrome c protein works in yeast (a unicellular organism) that has had its own native cytochrome c gene deleted, even though yeast cytochrome c differs from human cytochrome c over 40% of the protein (Tanaka et. al 1988a; Tanaka et al. 1988b; Wallace and Tanaka 1994)."
http://www.talkorigins.org/...ction4.html#protein_redundancy

Nearly every other amino acid is different between these two proteins. So why so much difference between these proteins when either sequence works just fine? They replaced yeast cytochrome c with human cytochrome c. The result? Perfectly healthy and functional yeast. So why would a designer change the sequence by 40% when no changes were needed? Even more, why change them to produce a nested hierarchy that mimics millions of years of evolution?

No it wouldn't. It would be much more effecient to use the same amino acid sequence in multiple species for the same function. It is even more effecient not to have to worry about changing the sequence to match an evolutionary history that never occurred.

But is it? It would seem to me that you need to support this argument. Why is it that yeast function just fine with a human copy of the cytochrome c gene? If the human cytochrome c sequence works just fine in yeast, then why use a different sequence that differs by 40%? Why keep using a different sequence for the same function when one sequence would have worked just fine?

All of them use the same oxidative cycle in their mitochondria. The cytochrome proteins serve the same exact function in each, and yet the sequence differs by 40% across those species. Nothing you have offered so far explains this from a design perspective. I will continue with my contention that these observations are contrary to what we would expect from a design process. It is equivalent to changing the car manuals for identical cars by 40% just because.

Again, they replaced yeast cytochrome c with human cytochrome c. The yeast chugged along happily just like they did with their own gene even though the genes differed by 40%. You need to include this observation in your explanations.

This still does not explain the observations as it relates to functional redundancy and protein sequence divergence.

Edited by Taq, : No reason given.

Message 223 of 373 (646577) 01-05-2012 11:47 AM

Reply to: Message 217 by foreveryoung 01-04-2012 7:30 PM

So why is it that we can replace yeast cytochrome c with human cytochrome c and the yeast are unaffected, even though the sequence differs by 40%? Why not use the same sequence for both organisms?

This would only apply to the promoter region of the cytochrome c gene, not the actual protein sequence.

We already know that yeast can use the human cytochrome c sequence. So why create more sequences than you need to?

Message 224 of 373 (646580) 01-05-2012 11:56 AM

Reply to: Message 213 by foreveryoung 01-04-2012 6:44 PM

No, it is a pattern of homology created by evolutionary mechanisms in species that do not participate in horizontal genetic transfer.

Then why does it mimic the pattern of homology that we observe evolution producing?

So we are ignoring the species with feathers and teats? Perhaps you could name this species for us?

A comparison of human, timber wolf, and tasmanian wolf cytochrome c will return a result where the human and timber wolf cytC share the most similarities while both are equidistant from the tasmanian wolf. This is exactly what we would expect to see if evolution were true. How does design predict this finding?

Message 225 of 373 (646582) 01-05-2012 12:11 PM

Reply to: Message 213 by foreveryoung 01-04-2012 6:44 PM

You can see it for Cyt B at Message 17 in my thread Confidence in evolutionary science, and you are welcome to perform the same work I did but for Cyt C at your leisure (the tools are out there and they are free to use).

Edited by Modulous, : No reason given.

Message 226 of 373 (647059) 01-08-2012 12:21 AM

Reply to: Message 170 by bluegenes 01-02-2012 4:15 AM

The moment someone does that, then in a desperate attempt to find a loop hole, the conversation suddenly degrades into quibbling over the definition of words... to the point that you practically have to define the very word "DEFINE." Its all really quite very comical to watch.