"If ENCODE is right then Evolution is wrong"

[xianghua]

You sure about that?

yes im sure. can you give me a specific example and explain why we cant do it without evolution to be true? english isnt my native so im not sure i understand what they are refer to in those examples. so be specific.

 

[xianghua]

no. the claim that a fish evolved into human is a theory. not a fact.

 

[xianghua]

Figure 1 shows the correlation between the amount of coding sequence and complexity. I don't think that's what you're aiming for.

yep, sorry. take a look at figure 2-3:


A meta-analysis of the genomic and transcriptomic composition of complex life

It's quite possible, though, that the correlation actually does represent causation, at least in the case of multicellular organisms.

thanks. this is all we need.

 

[xianghua]

1. If you have your flu jab every year then you can thank evolution theory for that benefit to your health.

the flu virus is still a flu virus. so its not evolution but a variation.

 

[sfs]

thanks. this is all we need.

Why? The mechanism I suggested has nothing to do with intelligent design.

 

[pshun2404]

They are saying that "biochemically active" tells you very little about whether the DNA in question performs any useful function for the organism. Specifically, they are saying that the sequence content of much of that DNA does not matter at all for the organism -- for any measurable trait of the organism, for how well it survives and reproduces. What they're saying has nothing to do with protein-coding genes. It's been known for many decades that some non-coding DNA is functional, and it's been known since 2002 (when the mouse genome was analyzed) that most functional DNA in the human genome is noncoding. Every critic I've seen knows all of this stuff.

Who? Citations, please.

Sorry I misunderstood what you first posted. This first paragraph is exactly right and that was my actual point...non-coding sections are also essential and have purpose. When the junk concept first came out in the 70s a lot of hardliners saw it all as junk which it is not, that's all. And just to be clear I am not one who believes that if Encode is correct that Evolution is not.

But one indicator comes from Is junk DNA bunk? A critique of ENCODE, by W. Doolittle, which reads "There is much excitement in the blogosphere, among mainstream science journalists, and within the community of practicing genome biologists about a flurry of articles and letters in the September 6th, 2012 issue of Nature. These papers and many others published at about the same time and since under the umbrella of the ENCODE project collectively claim function for the majority of the 3.2 Gb human genome, not just the few percent already recognized as genes (traditionally defined) or obvious gene-controlling elements. Kolata writes in The New York Times that “[t]he human genome is packed with at least four million gene switches that reside in bits of DNA that were once dismissed as ‘junk’ but that turn out to play critical roles in controlling how cells, organs and other tissues behave” (1). In a Nature News and View commentary, Ecker et al. (2) assert that “[o]ne of the more remarkable findings described in the consortium’s entrée paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly ‘junk DNA.’” The editors of The Lancet (3) enthuse: “Far from being ‘junk,’ the DNA between protein encoding genes consists of myriad elements that determine gene expression, whether by switching transcription on or off, or by regulating the degree of transcription and consequently the concentrations and function of all proteins.” Succinctly, in Science, Pennisi (4) declares that the ENCODE publications write the “eulogy for junk DNA.”

And I also got that same impression from the following two articles (though that was not their main point)


Is junk DNA bunk? A critique of ENCODE

http://www.nature.com/news/form-and-function-1.12580

 

[pshun2404]

The arrogance of creationists is truly breathtaking. They actually think they can tell a working biologist to do his biology homework?

No one can read everything and express all peoples opinions even "working biologists"!

 

[lesliedellow]

No one can read everything and express all peoples opinions even "working biologists"!

Somebody who has spent years in a laboratory at a famous university doubtless knows a great deal more than the competely unqualified creationist who tells him to do his homework.

 

[sfs]

When the junk concept first came out in the 70s a lot of hardliners saw it all as junk which it is not, that's all.

Again, who?

But one indicator comes from Is junk DNA bunk? A critique of ENCODE, by W. Doolittle, which reads

Nothing in there suggests that only coding sequence is functional.

 

[pshun2404]

Again, who?

Nothing in there suggests that only coding sequence is functional.

No...you are right, not only...I realize that the majority of trait-associated loci, including ones that contribute to human diseases and susceptibility, also lie outside protein-coding regions

Most scientists agree that “These findings suggest that the noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse gene regulatory and other functions.”

Defining functional DNA elements in the human genome

In light of this, the earlier (less informed) “Junk” judgment is inaccurate to say the least. In time we may come to realize that every base pair exactly where it is located is essential and plays a necessary role. Now YES that is just an opinion but I believe it is reasonable.

The article linked goes on to say “Despite the pressing need to identify and characterize all functional elements in the human genome, it is important to recognize that there is no universal definition of what constitutes function, nor is there agreement on what sets the boundaries of an element. Both scientists and nonscientists have an intuitive definition of function, but each scientific discipline relies primarily on different lines of evidence indicative of function. Geneticists, evolutionary biologists, and molecular biologists apply distinct approaches, evaluating different and complementary lines of evidence. The genetic approach evaluates the phenotypic consequences of perturbations, the evolutionary approach quantifies selective constraint, and the biochemical approach measures evidence of molecular activity. All three approaches can be highly informative of the biological relevance of a genomic segment and groups of elements identified by each approach are often quantitatively enriched for each other.”

In my opinion, such differences in perspective can and do lead to different definitions of what constitutes “functional”.

“Some of these differences stem from the fact that function in biochemical and genetic contexts is highly particular to cell type and condition, whereas for evolutionary measures, function is ascertained independently of cellular state but is dependent on environment and evolutionary niche. The methods also differ widely in their false-positive and false-negative rates, the resolution with which elements are defined, and the throughput with which they can be surveyed.”

So we agree that the genome is fully active with little or few (if any) segments that are actually JUNK!

 

[PsychoSarah]

the flu virus is still a flu virus. so its not evolution but a variation.

-_- viruses evolve, since they have genetic material subject to mutation. Hence how ENTIRELY NEW diseases appear from time to time. However, the variation in viral mutation frequency is quite extreme compared to living organisms, for reasons of differences in replication and chemical stability. The rabies virus is so stable that we can recognize records of it from thousands of years ago by symptom descriptions. In contrast, HIV changes so frequently that treatment has to be tailored from person to person.

However, thanks to the limited genes a virus has and the predictable selection pressures they are subject to, it's easy to make vaccines for viruses that don't change super fast, such as the chicken pox and flu viruses. The faster the virus changes, the more frequently vaccines are needed to keep up. For the most part, some of them change so slowly that our acquired immunity will give out before they mutate enough to actually get around it.

 

[Bugeyedcreepy]

Gravity is repeatable and testable. Perhaps you can enlighten me by repeating and demonstrating how an ape-like creature evolves into a human.

Do you accept that a paternity test is valid? Do you accept that forensic DNA Matching is definitive beyond a reasonable doubt? Because rational people do. If you do, then that there is the justification to accept that those exact same methods are used to determine our relatedness to all other living things. Further, ERVs are another key genetic indicator that makes it irrational to not accept the evidence. The exact pattern of matching endogenous retroviral insertions, along with the endogenous retroviral insertions that don't match between us and the other great apes, and further on to all other life on this planet push this point beyond any reasonable doubt.

Yet you read "opinion pieces" by sfs, Subduction Zone, and Tim Minchin?

No. Go back and read what I said. They've pointed out valid scientific research that shows otherwise. I didn't cite their opinions.

 

[Subduction Zone]

Since I was mentioned in the following post I am responding to it:

Gravity is repeatable and testable. Perhaps you can enlighten me by repeating and demonstrating how an ape-like creature evolves into a human.

The tests for gravity are repeatable and testable. The tests that tell us that we evolved from other apes are also repeatable and testable. Your demand demonstrates that you do not fully understand the scientific method. There are countless events that occur only once, yet they can be verified by applying the scientific method. Evolution is a one time event so demanding that an exact result be repeated only demonstrates that one understands neither evolution nor the scientific method.

Yet you read "opinion pieces" by sfs, Subduction Zone, and Tim Minchin?

I don't write "opinion pieces". I will link to valid sources and there are some aspects of science that I can explain. Though most creationists run away from a one on one explanation. But I don't think that I have ever linked Tim Minchin here. He is an excellent pianist and writes a fair schtick of poetry. But I would not call him an expert in the sciences. And he uses a few to many "bad words" to be linked to from this site.

 

[pitabread]

yes im sure.

That was a rhetorical question. It's a fact that evolutionary biology has been integrated into the modern development of medicine.

can you give me a specific example and explain why we cant do it without evolution to be true? english isnt my native so im not sure i understand what they are refer to in those examples. so be specific.

Are you familiar with phylogenetic trees?

For example:

These describe evolutionary relationships of organisms. What has been happening in genomics for the last decade or so, is researchers have been overlaying data derived from these evolutionary relationships (the phylogenetic trees) into genomic research when comparing and analyzing different genomes. This allows them to make more informed analyses of the genomes particularly when it comes to making identification of functional genome regions, predictions about gene functions, etc. If you want to read more, Wikipedia has a page on it: Phylogenomics - Wikipedia

In turn, these techniques are being used in pharmacology for discovering therapeutic targets as part of the drug discovery process: Drug discovery - Wikipedia

Here's another paper with respect to plant biology, evolution, and medicine in this context:

Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life

 

[Bugeyedcreepy]

There is no such thing as random other than unpredictability due to ignorance.
For example, quantum fluctuations are considered random because the source
of the timing is unknowable.

Random number generators can be produced using Pi, but it is actually a known and rigid number set.

There's plenty of ways to engineer (...create?) random number generators although you're right in that they aren't truly random. That said, for the application and method that they're employed in, they can be considered properly random. In fact, I can write and present you one if you like, I challenge you to predict its output and we'll see how we go?

 

[sfs]

Most scientists agree that “These findings suggest that the noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse gene regulatory and other functions.”

Sure. But most scientists also already knew that.

In light of this, the earlier (less informed) “Junk” judgment is inaccurate to say the least.

Wbat earlier and less informed junk judgment? You keep suggesting that scientists used to have badly mistaken ideas about junk DNA, but you've provided no evidence of that.

In time we may come to realize that every base pair exactly where it is located is essential and plays a necessary role. Now YES that is just an opinion but I believe it is reasonable.

All the evidence we have -- including the evidence from ENCODE -- suggests that your opinion is wrong.

In my opinion, such differences in perspective can and do lead to different definitions of what constitutes “functional”.

Sure, there indeed subtleties to the concept of "function", and some very fuzzy cases. None of that changes the fact that the definition ENCODE used was dumb.

So we agree that the genome is fully active with little or few (if any) segments that are actually JUNK!

Who are you agreeing with? I agree that most of the genome is biochemically active (heck, the whole thing is replicated and that's biochemical activity, so it all must be functional), and that most of the genome is also junk.

[Edited to fix one of my sentences, which somehow came out wackbard.]

 

[Subduction Zone]

There's plenty of ways to engineer (...create?) random number generators although you're right in that they aren't truly random. That said, for the application and method that they're employed in, they can be considered properly random. In fact, I can write and present you one if you like, I challenge you to predict its output and we'll see how we go?

Are you familiar with this project:

Tree of Life Web Project

They are trying to build as inclusive of a Tree of Life as possible.

 

[xianghua]

Why? The mechanism I suggested has nothing to do with intelligent design.

who is talking now about id? we only talk about the functionality of the genome.

 

[Lily of Valleys]

Do you accept that a paternity test is valid? Do you accept that forensic DNA Matching is definitive beyond a reasonable doubt? Because rational people do. If you do, then that there is the justification to accept that those exact same methods are used to determine our relatedness to all other living things. Further, ERVs are another key genetic indicator that makes it irrational to not accept the evidence. The exact pattern of matching endogenous retroviral insertions, along with the endogenous retroviral insertions that don't match between us and the other great apes, and further on to all other life on this planet push this point beyond any reasonable doubt.

You have brought up a very important point. The disagreement is not with the evidence, but the interpretation of the evidence.

All these DNA matching exercises are based on the assumption that similarities mean common descent, which doesn't pose any problem with paternity test since it is an established fact that human does reproduce human, or forensic DNA matching, which is comparing DNA between humans. But it becomes circular reasoning to state that based on the assumption that similarities between different kinds mean common descent, therefore if they are similar it proves common descent.

This article lays out in details how ERV does not prove common descent any more than common design:

Do Endogenous Retroviruses (ERVs) Support Common Ancestry?

No. Go back and read what I said. They've pointed out valid scientific research that shows otherwise. I didn't cite their opinions.

Well, if you go back to check their posts before where you mentioned them, none of them cited any links.

My point is, as far as I am aware, none of the posts on this forum are peer reviewed paper, what everyone said are simply their opinions, in your word "opinion pieces", yet you still read them, right? Then what's wrong with reading other "opinion pieces" outside of this forum?

Peer-reviewed paper are not necessarily fool-proof, non-peer-reviewed opinions are not necessarily invalid. Whether peer-reviewed or non-peer-reviewed, what matters is whether their points are valid, not where they come from.

 

[Lily of Valleys]

Since I was mentioned in the following post I am responding to it:

You were only mentioned because Bugeyedcreepy mentioned you.

Though most creationists run away from a one on one explanation.

People would be more likely to engage in a conversation with you if you address only the points but not the person.

And no, I am not interested in having an argument with you. ad hominem is boring.

But I don't think that I have ever linked Tim Minchin here. He is an excellent pianist and writes a fair schtick of poetry. But I would not call him an expert in the sciences. And he uses a few to many "bad words" to be linked to from this site.

No one said you linked Tim Minchin. The post wasn't addressed to you, it was addressed to Bugeyedcreepy.