"If ENCODE is right then Evolution is wrong"

[PsychoSarah]

Can you read and think logically? Seems like it.
I am as capable of Googling any matter and finding
the facts as any PhD. More than some I have known.

While anyone can Google search, having access to information is not the same thing as understanding it. Furthermore, there is a bit of an art to recognizing the difference between a reliable source and garbage. Do you understand how annoying it is for people to source National Geographic as if it is a scientific journal? Certain concepts in biology need some basic understanding of them to even know what to type into a search engine.

It's the geeks who are masters of the information age,
as were the bookworms of the past.

Pretty sure Genghis Khan didn't conquer such a vast area because he was the most well-read guy around XD

 

[tas8831]

Birney admitted - in a blog post, of all places, in which he was pretending to interview himself - that the 80% was basically used to impress the rubes

ENCODE: My own thoughts - Ewan's Blog: Bioinformatician at large

Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?

A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.​

Another ENCODE researcher also indicated that the real, evidence-based number is much lower:

Max Libbrecht on ENCODE’s results regarding junk DNA. « Genomicron

"In its press releases, ENCODE reported finding 80% of the genome with “specific biochemical activity”, which turned into (through some combination of poor presentation on the part of ENCODE and poor interpretation on the part of the media) reports that 80% of the genome is functional. This claim is unlikely given what we know about the genome (here is a good explanation of why), so this created some amount of controversy....
I think very few members of ENCODE believe that the consortium proved that 80% of the genome is functional; no one claimed as much on the reddit AMA, and Ewan Birney has made it clear on his blog that he would not make this claim either. ..."

 

[tas8831]

While anyone can Google search, having access to information is not the same thing as understanding it.

EXACTLY.

 

[tas8831]

There are at least three things that indicate lots more research has to be done on this issue:"[/i]
An Explanation that is Not Exactly Iron-Clad – Proslogion

Jay Wile's background is in nuclear chemistry. How do you know that what Wile claims is accurate?

I'll get back to junk DNA in another post later.

Great - more from Wile's blog?

 

[Loudmouth]

Birney admitted - in a blog post, of all places, in which he was pretending to interview himself - that the 80% was basically used to impress the rubes

I don't think that is the whole picture. What they did was show that 80% of the genome does something that they and others find interesting, and I think that is worthwhile information for those who study the human genome. However, they went too far when they called it "functional", because that word carries a lot of baggage with it. So it really isn't the percentage that is the problem. Rather, it is how they labelled that 80%.

Is there a bit of salesmanship in scientific papers? Absolutely. Do some authors use too much salesmanship? Absolutely, and the ENCODE paper is probably one of them. However, we shouldn't throw the baby out with the bathwater.

 

[tas8831]

Now, back to the quote about Avida.

" As Dr. John Sanford demonstrated a while ago, the “gold standard” digital simulation of evolution (Avida), requires at least 85% of the starting genome to be junk in order to produce any significant evolution. "

In other words, unless you specify >85% junk DNA, you do not get any significant evolution.
No bacteria to man. Not even bacteria to paramecium.

Please explain how you know that "Dr.John Sanford" was CORRECT.

 

[tas8831]

I don't think that is the whole picture. What they did was show that 80% of the genome does something that they and others find interesting, and I think that is worthwhile information for those who study the human genome. However, they went too far when they called it "functional", because that word carries a lot of baggage with it. So it really isn't the percentage that is the problem. Rather, it is how they labelled that 80%.

Is there a bit of salesmanship in scientific papers? Absolutely. Do some authors use too much salesmanship? Absolutely, and the ENCODE paper is probably one of them. However, we shouldn't throw the baby out with the bathwater.

Well of course - they have accumulated a huge amount of very useful data. Birney's formulation of "functional", however, reminds me very much of Feyerabend's characterization of the rantings of ancient soothsayers as equal to science...

 

[pat34lee]

So if you wanted to be a master of Quantum Field Theory, all you would have to do is read a Wikipedia article on the subject, and you would be as knowledgable as any PhD physicist?

I have heard some idiotic claims, but yours takes the biscuit.

Comprehension sorely lacking, it seems.
One can only conclude it is by intention.

 

[pat34lee]

Please explain how you know that "Dr.John Sanford" was CORRECT.

By the one pertinent word in the quote:
DEMONSTRATED
He proved it by doing it.

 

[pat34lee]

Pretty sure Genghis Khan didn't conquer such a vast area because he was the most well-read guy around XD

Khan lived in a pre-industrial world.
Even 20 years ago, the world was different.

 

[pat34lee]

Jay Wile's background is in nuclear chemistry. How do you know that what Wile claims is accurate?

Great - more from Wile's blog?

No, I'm tired of researching. I should do like some
of the others here and make comments with nothing
to back them but sarcasm.

 

[Subduction Zone]

By the one pertinent word in the quote:
DEMONSTRATED
He proved it by doing it.

Where? Since when did he do any work in abiogensis at all? Please link the peer reviewed article from an appropriate well respected professional source .

 

[Subduction Zone]

No, I'm tired of researching. I should do like some
of the others here and make comments with nothing
to back them but sarcasm.

When all you can do is to cite bogus sources you should not complain about the sarcasm that you earn.

 

[lesliedellow]

Comprehension sorely lacking, it seems.
One can only conclude it is by intention.

No lack of comprehension on my part. Somebody who failed high school biology trying to lecture a working biologist.

 

[sfs]

Going back to one, though and junk DNA.

" As Dr. John Sanford demonstrated a while ago, the “gold standard” digital simulation of evolution (Avida), requires at least 85% of the starting genome to be junk in order to produce any significant evolution. "
Junk DNA and Evolution – Proslogion

I'd lost track of this thread. Here's a challenge. Where in Sanford's paper (which is here) does he show that 85% of the genome has to be junk?

 

[PsychoSarah]

Khan lived in a pre-industrial world.
Even 20 years ago, the world was different.

-_- Donald Trump is not the president of the United States because he is the most well-read guy around. In fact, I challenge you to find a single world leader that has the best education compared to everyone else within their country.

 

[tas8831]

Facts from folks who believe their Gramdma's are 99% Chimp and have a common ancestor with an onion?

Facts from folks who believe their ancestor was dust of the ground and think that the Ten Commandments are the basis for the Constitution?

 

[Gene2memE]

Now, back to the quote about Avida.

" As Dr. John Sanford demonstrated a while ago, the “gold standard” digital simulation of evolution (Avida), requires at least 85% of the starting genome to be junk in order to produce any significant evolution. "

In other words, unless you specify >85% junk DNA, you do not get any significant evolution.
No bacteria to man. Not even bacteria to paramecium.

Nope - there's nothing in Dr Sanfords original paper that would lead to that conclusion. Zero. Zip. Nada.

I even quoted the relevant parts for you.

Who are you going to believe - the original author, or the creationist apologist re-interpreting the article?

 

[tas8831]

By the one pertinent word in the quote:
DEMONSTRATED
He proved it by doing it.

Um... No, he really did not do it.

And you did not answer the question - i asked how YOU know that Sanford is correct. Sanford and his acolytes CLAIM he is correct, but how do YOU know that he is?

You are just taking his word for it, which is what people like him expect.