"If ENCODE is right then Evolution is wrong"

[Seejer]

first, evolution isnt a fact but a theory.

 

[Subduction Zone]

I csn see then how many according to you believe these lies. Probably our schools are to blame for the heresy of evolution.

How can a fact be "heresy"?

 

[pitabread]

evolution doesnt have any connection to making medicine

You sure about that?

Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as antibiotic resistance spreads, a challenge that may better faced by unveiling chemical diversity produced by microbes. Current microbial genome mining approaches have revitalized research into antibiotics, but the empirical nature of these methods limits the chemical space that is explored. Here, we address the problem of finding novel pathways by incorporating evolutionary principles into genome mining.

Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes | bioRxiv

Phylogenomics, which advocates an evolutionary view of genomic data, has been useful in the prediction of protein function, of significant sequence and structural elements, and of protein interactions and other relationships. Although such information is important in characterizing individual pharmacological targets, evolutionary analyses also indicate new ways to view the overall space of gene products in terms of their suitability for therapeutic intervention. This view places increased emphasis on the comprehensive analysis of the evolutionary history of targets, in particular their orthology and paralogy relationships, the rate and nature of evolutionary change they have undergone, and their involvement in evolving pathways and networks.

Pharmacophylogenomics: genes, evolution and drug targets : Abstract : Nature Reviews Drug Discovery

 

[sfs]

take a look at figure 1.

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

there is a great correlation between complexity (in terms of cell types number) and the amount of suppose junk.

No, there's a correlation between the complexity and the amount of noncoding DNA. No one has ever suggested that all noncoding DNA was junk. The paper says nothing at all about what fraction of the genome might actually be functional in any meaningful sense (although their willingness to accept the ENCODE definition of "functional" is not encouraging), just that more complex organisms tend to have larger genomes.

It's rather disappointing that the paper doesn't consider alternative sources of such a correlation. For example, species that are low in complexity typically have short generation times and very large population sizes. The former means that they are under stronger selective pressure for small genomes, and the latter means that selection is more effective.

It's quite possible, though, that the correlation actually does represent causation, at least in the case of multicellular organisms. Transposons represent an important source of regulatory elements, and it may be that lineages with a lot of transposons (and therefore large genomes) have an easier time evolving new cell types and greater complexity.

There is at present zero evidence that I'm aware of that most of the human genome has any effect on anything that matters.

 

[bhsmte]

evolution doesnt have any connection to making medicine, we can still made a medicine even if evolution is wrong.

Evolutionary theory, has played a huge role in modern medicine.

 

[tyke]

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

 

[Lily of Valleys]

Well, evolution is a fact - what is it about this combination of blogs, media releases and opinion pieces leads you to believe that the actual scientific research papers don't entirely support evolution? Perhaps you could pull up this peer reviewed research paper & point out the section to support this position?

Any theory that can potentially be proven wrong cannot be a fact. But if anyone like to believe a theory to be a fact, to each their own.

Of course Dan Graur is an evolutionist, it is no surprise that he wants to prove ENCODE wrong, but I am only interested in the data and their implication, not so much about individual scientist's position.

The ENCODE Embroilment, Part II by Casey Luskin

 

[Subduction Zone]

Any theory that can potentially be proven wrong cannot be a fact. But if anyone like to believe a theory to be a fact, to each their own.

Of course Dan Graur is an evolutionist, it is no surprise that he wants to prove ENCODE wrong, but I am only interested in the data and their implication, not so much about individual scientist's position.

The ENCODE Embroilment, Part II by Casey Luskin

Casey Luskin is not a biologist at all and has no clue about the science. And sfs already explained why project ENCODE overstated their accomplishments. He is a biologist.

And no, theories can be wrong and yet they can describe facts. They do that all of the time. The theory of gravity may be wrong, but I doubt if you would say that gravity is not a fact.

Your side lost over 100 years ago. Instead of grasping at straws and listening to dishonest people such as Luskin you should be trying to find out why we know that we are the product of evolution.

 

[pshun2404]

Except Graur and ENCODE are using completely different meanings of "functional". In fact, Graur's point is that ENCODE's definition is ridiculous. ENCODE defines "functional" as "biochemically active", which actually says very little about whether the DNA does the organism any good or not. For example, introns are chunks of DNA in genes that are transcribed into RNA, and then chopped out and discarded to form the mature messenger RNA that will end up producing proteins. But ENCODE counts all introns as functional because they are transcribed. Graur is right: it's a dumb definition of "functional".

The best estimate we have of the fraction of the human genome that has a function in the ordinary sense -- that affects how well people can survive and reproduce -- also comes from the ENCODE project, from the paper by Kellis and colleagues. They put the fraction around 11%, as I recall.

Yeah I read Kellis's assessment as well and none of the ENCODE consortium has formed "final conclusions" yet. But I believe that aside from this hypothesis driven field (that interprets much data via the hypothesis rather than letting it shape the hypothesis) the definition of "functional" as only being accepted to mean "encodes for proteins" is a means to dwarf progress and limit the science ot only one conclusion (that which supports the already pre-supposed hypothesis).

I get the impression that most of the ENCODE scientists (most of whom believe in evolution) agree not to limit the meaning into this little prejudiced box, and use the meaning that "functional" equals having meaningful or useful purpose.

The REAL non-hypothesis corrupted definition of "functional" means "of or having a special activity, purpose, or task; relating to the way in which something works or operates". The reason for Grauer and other's over-reacting is because some of the implications of the results being uncovered by this non-prejudiced group of over 450 world class scientists is bringing some of their accepted hypothesis driven interpretations into question.

"Functional" does NOT MEAN "encodes for proteins"...So let us guard against them being able to pour new meaning or change the meaning of this commonly understood term so they can make their pre-suppositions APPEAR to be established truths (especially if you are a scientist).

 

[Bugeyedcreepy]

Any theory that can potentially be proven wrong cannot be a fact. But if anyone like to believe a theory to be a fact, to each their own.

Evolution is both a theory and a fact in exactly the same way that Gravity is both a theory and a fact. What's more, we know more about Evolution than we do Gravity. Your statement reminds me of a Tim Minchin quote about people who say "Evolution is only a Theory"...

Of course Dan Graur is an evolutionist, it is no surprise that he wants to prove ENCODE wrong, but I am only interested in the data and their implication, not so much about individual scientist's position.

The ENCODE Embroilment, Part II by Casey Luskin

As has been pointed out by @sfs and @Subduction Zone , there are quite a lot of reasons to safely set aside such opinion pieces by unqualified armchair enthusiasts as this one you've included...

 

[sfs]

the definition of "functional" as only being accepted to mean "encodes for proteins" is a means to dwarf progress and limit the science ot only one conclusion (that which supports the already pre-supposed hypothesis).

In 18 years of doing genetics, the only person I've ever seen suggest that "functional" means only "encodes for proteins" is you.

The REAL non-hypothesis corrupted definition of "functional" means "of or having a special activity, purpose, or task; relating to the way in which something works or operates". The reason for Grauer and other's over-reacting is because some of the implications of the results being uncovered by this non-prejudiced group of over 450 world class scientists is bringing some of their accepted hypothesis driven interpretations into question.

No, the reason Graur and many other biologists were upset with ENCODE was that they chose the word "functional" to describe results that probably had very little to do with function -- and then issued press releases that equivocated between their biochemical definition and the ordinary language one. They produced (mostly) valid results about biochemical activity and implied that they meant something different.

 

[pshun2404]

In 18 years of doing genetics, the only person I've ever seen suggest that "functional" means only "encodes for proteins" is you.

You really need to do more homework. In your opinion (or from what you have read) what do those who are accusing the ENCODE project of using a false or inadequate definition of "functional" saying? I have read about 9 or 10 and many imply that because these alleged "Junk" sections are not part of functional genes (which code for proteins) they have no real "function". School me please....

 

[Lily of Valleys]

Evolution is both a theory and a fact in exactly the same way that Gravity is both a theory and a fact. What's more, we know more about Evolution than we do Gravity. Your statement reminds me of a Tim Minchin quote about people who say "Evolution is only a Theory"...

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

As has been pointed out by @sfs and @Subduction Zone , there are quite a lot of reasons to safely set aside such opinion pieces by unqualified armchair enthusiasts as this one you've included...

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

 

[pitabread]

Gravity is repeatable and testable.

Do you know that there is still scientific debate over what gravity actually *is*?

 

[sfs]

You really need to do more homework. In your opinion (or from what you have read) what do those who are accusing the ENCODE project of using a false or inadequate definition of "functional" saying?

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.

I have read about 9 or 10 and many imply that because these alleged "Junk" sections are not part of functional genes (which code for proteins) they have no real "function".

Who? Citations, please.

 

[lesliedellow]

You really need to do more homework.

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

 

[bhsmte]

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

Agree. But as deep as they are dug in and invested in their beliefs, they really have no choice to defend their belief at all costs. Acknowledging well evidenced reality, is far too painful.

 

[Lily of Valleys]

Do you know that there is still scientific debate over what gravity actually *is*?

Not surprising. There are many things science doesn't have an answer for. Science is useful but is not the be-all and end-all of everything.

 

[SkyWriting]

Given no engineer is apparent, not surprised...

EDIT: That said, engineers build in random components all the time - often there's a requirement for it.

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.

 

[SkyWriting]

Pray tell, give me one example of how the THEORY of. evolution impacts human welfare and the economy

The worlds supply of food has been dependent on artificial "natural selection"
though the direction is moving toward direct manipulation of genes in both
plant and animals.

Health care is based on transmission rates of disease and pathogens
and how the body reacts to treatments. Birth rates are manipulated
based on economic theory.