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A Creationism Prediction Being Fullfilled


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#101 Arch

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Posted 17 June 2009 - 12:03 AM

Hi guys,

I know it's about 4 pages too late, but ikester mentioned that we've now found a use for the appendix. I wasn't aware this had happened. I just did a quick search for such uses and there seem to be studies being done into its use, but nothing conclusive yet.

Does ikester or anyone else have some additional info on this topic? I'd be most appreciative :(

Regards,

Arch.

#102 jason777

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Posted 17 June 2009 - 01:26 AM

Hi guys,

I know it's about 4 pages too late, but ikester mentioned that we've now found a use for the appendix. I wasn't aware this had happened. I just did a quick search for such uses and there seem to be studies being done into its use, but nothing conclusive yet.

Does ikester or anyone else have some additional info on this topic? I'd be most appreciative  :(

Regards,

Arch.

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Hi Arch,

In September, a team of surgeons and immunologists at Duke University proposed a reason for the appendix, declaring it a “safe house” for beneficial bacteria. Attached like a little wiggly worm at the beginning of the large intestine, the 2- to 4-inch-long blind-ended tube seems to have no effect on digestion, so biologists have long been stumped about its purpose. That is, until biochemist and immunologist William Parker became interested in biofilms, closely bound communities of bacteria. In the gut, biofilms aid digestion, make vital nutrients, and crowd out harmful invaders. Upon investigation, Parker and his colleagues found that in humans, the greatest concentration of biofilms was in the appendix; in rats and baboons, biofilms are concentrated in the cecum, a pouch that sits at the same location.

The shape of the appendix is perfectly suited as a sanctuary for bacteria: Its narrow opening prevents an influx of the intestinal contents, and it’s situated inaccessibly outside the main flow of the fecal stream. Parker suspects that it acts as a reservoir of healthy, protective bacteria that can replenish the intestine after a bacteria-depleting diarrheal illness like cholera. Where such diseases are rampant, Parker says, “if you don’t have something like the appendix to harbor safe bacteria, you have less of a survival advantage.”


http://discovermagaz...endix-explained - 48k -

#103 Guest_Keith C_*

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Posted 18 June 2009 - 06:16 PM

AFP and AFGP are the same.  The antarctic fish uses AFGP and that was primary topic on this thread: all the papers on both sides was discussing this fishes AFP (or AFGP) protein.

AFPs and AFGP lower the freezing point of blood and enable fish capable of producing one of these to survive in extremely cold seawater. However they are different chemically and produced as a result of different genes.
Glycoproteins are different from proteins.

I discussed this very figure in detail.  In fact the image you just posted came from my posting.

What you did was repeat your assertion that AFP genes were produced by gene duplication followed by deletion, despite the fact that the figure you pasted clearly indicated much more than those 2 steps.

Kieth your biggest complaint is about semantics: AFP or AFGP.

You never addressed the bigger issues:

1) AFGP as a sloppy folded protein.
2) AFGP has no interactions with other proteins.
3) AFGP length is variable.  That precision that hallmarks most proteins and life in general is not evident with AFGP.

Therefore, AFGP is exactly what it is.  A digestive enzyme that was duplicated and then underwent deletions.  It is not a mutation sequence that is building a new system or anything new or novel. It is not coordinating with anything and is far less sophisticated than the digestive enzyme is was created from.  Therefore, no new information was created.

AFGP is an entirely original short glycoprotein, required to be present in high concentration. The gene to produce it has an innovative structure, one start sequence followed by 41 code sequences separated by spacer sequences which are eventually removed. Gene from this species produces a single AFGP structure. Other species produce slightly different molecules, and different copy numbers.

AFGP is suited to its function. Short protein with flexibility, and present in high concentration is efficient. Function requires interaction with ice surfaces, not other proteins. Why produce a longer, more rigidly folded protein when it would be less effective.
Variable length is hallmark of the AF proteins.

Origin of AFGP and the AFPs are probably different. The Arctic ice-cap began to form around 20 million years ago, while freezing of Arctic started around 4 million years ago. AFPs are found in Northern fish species and presumably evolved there, AFGP is present in one large group (122 species) of mainly Southern fish. The few northern varieties are presumably derived by migration from the southern radiation.

What really characterizes proteins and enzymes is that they are very well adapted to their function. AFGP follows in that tradition, even if it does not satisfy Bruce's aesthetic sense.

#104 Guest_Keith C_*

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Posted 18 June 2009 - 08:02 PM

This item:-
"What is the function of the human appendix? Did it once have a purpose that has since been lost? "
http://www.scientifi...e-function-of-t
lists several uses for the appendix.

The last use, as a source of spare parts for reconstructive surgery, shows the designer's forethought in providing this organ.

#105 Bruce V.

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Posted 18 June 2009 - 08:04 PM

AFPs and AFGP lower the freezing point of blood and enable fish capable of producing one of these to survive in extremely cold seawater.  However they are different chemically and produced as a result of different genes.
Glycoproteins are different from proteins.

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Keith,

We have only been talking about AFGP which is under the subcategory of AFP. I have only been talking about the AFP in the Antarctic Fish and so have you
NOTICE THE TITLE ON THE PAPER YOU POSTED!!


Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid  fish


From the paper:

The elucidation of how a notothenioid pancreatic trypsinogen gene was transformed into an AFGP gene provides the first clear and plausible evolutionary process by which one of the four known types of antifreeze proteins arose

Antifreeze protein stands for AFP.

From Wiki

There are many known non-homologous types of AFP.

Fish AFPs

Antifreeze glycoproteins or AFGPs are found in Antarctic notothenioids and northern cod. They are 2.6-3.3 kD.[5]



Notice under the heading of fish AFP the list the Antarctic notothenioids AFGP. Everything I have discussed was about this fishes mutation. I called it AFP but I could have called it AFGP.

I will not repeat myself again.

What you did was repeat your assertion that AFP genes were produced by gene duplication followed by deletion, despite the fact that the figure you pasted clearly indicated much more than those 2 steps.

What really characterizes proteins and enzymes is that they are very well adapted to their function.  AFGP follows in that tradition, even if it does not satisfy Bruce's aesthetic sense.

View Post


This is what I posted:

When a specific digestive enzyme was being created the process stuttered and created multiple copies of itself yielding a simple 3 amino acid repeat from a 9 nucleotide region. This is called gene duplication. Later some of the non-functioning parts of gene duplication were deleted. A later decedent of this fish had a second shuddering of this nine nucleotide region followed by deletions. The second set of mutations probably made AFP more stable.


Notice, I did take into account more than just 2 steps.

I am so tired of chasing phantom arguments. We are debating semantics not science. You have not yet addressed the core issue that this AFGP protein is less sophisticated that the digestive enzyme that it evolved from; that AFPG is sloppy folded and does not interact with other proteins or body systems. Therefore, this mutation shows how a loss of information can sometimes have a useful application. However, it does not show an increase in information, or that AFGP has any potential for building something new or novel like a new protein- protein interaction. The reason is because it doens't and it can't.

I am done with this debate.

#106 deadlock

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Posted 23 July 2009 - 02:24 PM

Not 'Genomic Junk' After All: LincRNAs Have Global Role In Genome Regulation
ScienceDaily (July 20, 2009) — Earlier this year, a scientific team from Beth Israel Deaconess Medical Center (BIDMC) and the Broad Institute identified a class of RNA genes known as large intervening non-coding RNAs or "lincRNAs," a discovery that has pushed the field forward in understanding the roles of these molecules in many biological processes, including stem cell pluripotency, cell cycle regulation, and the innate immune response.

But even as one question was being answered, another was close on its heels: What, exactly, were these mysterious molecules doing?

They now appear to have found an important clue. Described in the July 14 issue of the Proceedings of the National Academy of Sciences (PNAS) the scientific team from BIDMC and the Broad Institute shows that lincRNAs – once dismissed as "genomic junk" – have a global role in genome regulation, ferrying proteins to assist their regulation at specific regions of the genome.

"I like to think of them as genetic air traffic controllers," explains co-senior author John Rinn, PhD, a Harvard Medical School Assistant Professor of Pathology at BIDMC and Associate Member of the Broad Institute. "It has long been a mystery as to how widely expressed proteins shape the fate of cells. How does the same protein know to regulate one genomic location in a brain cell and regulate a different genomic region in a liver cell? Our study suggests that in the same way that air traffic controllers organize planes in the air, lincRNAs may be organizing key chromatin complexes in the cell."

Inspired by a lincRNA called HOTAIR -- which is known to bind key chromatin modifier proteins and to assist in getting these proteins to the proper location in the genome – the researchers hypothesized that other lincRNA molecules might be playing similar roles.

"DNA wraps around partner proteins to form a structure called chromatin, which affects which genes are 'turned on' and which are 'turned off'," explains first author Ahmad Khalil, PhD, a scientist in the Department of Pathology at BIDMC and the Broad Institute. "Chromatin does this through a process of compaction; by determining which areas to compact and which to leave open, chromatin successfully determines which genes are accessible for transcription."

But he adds, it has been a mystery as to how this chromatin structure is so precisely targeted by specific enzymes – and not others.

"By utilizing a technology known as RIP-Chip we were able to examine RNA-protein interaction on a large scale and determine which lincRNAs are associated with each enzyme we examined," he adds. To analyze this tremendous amount of data, coauthor Mitchell Guttman, PhD, a bioinformatician at BIDMC and the Broad Institute, used a mathematical algorithm that identified which lincRNAs are bound by chromatin-modifying enzymes and which are not.

"This analysis revealed that 20 to 30 percent of lincRNAs are bound by three distinct chromatin-modifying complexes," adds Khalil. "By depleting several of these lincRNAs from cells, we were able to show a significant overlap between the genes which become affected by the depletion of lincRNAs and the depletion of the enzymes. This provided us with the evidence that these proteins work together with lincRNAs to target specific regions of the genome."

Standard "textbook" genes encode RNAs that are translated into proteins, and mammalian genomes contain about 20,000 such protein-coding genes. Some genes, however, encode functional RNAs that are never translated into proteins. These include a handful of classical examples known for decades and some recently discovered classes of tiny RNAs, such as microRNAs. By contrast, lincRNAs are thousands of bases long. Because only about 10 examples of functional RNAs were previously identified, they seemed more like genomic oddities than key players. With these latest findings, which also uncovered an additional 1,500 lincRNAs, it's clear these RNA molecules are no mere messengers – they have demonstrated that they can and do play a leading role.

"Much work still remains to be done but we could one day envision utilizing RNA to guide personalized stem cells to specific cell fates to restore diseased and degenerative disease tissues," notes Rinn.

“Genomic Junk” Is Cell’s Air-Traffic Control




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