"If ENCODE is right then Evolution is wrong"

[pat34lee]

PRATT's.

Previous refutations also refuted.

 

[pat34lee]

ROFLOL! Part there in bold italics - Does he even know he's talking to @sfs??

Impressed? Any expert should have no trouble actually
making sense when they try to refute the facts, instead
of making light of them and sidestepping. With, you know,
something like proof. Links and/or quotes.

 

[Bugeyedcreepy]

Impressed? Any expert should have no trouble actually
making sense when they try to refute the facts, instead
of making light of them and sidestepping. With, you know,
something like proof. Links and/or quotes.

@sfs, a Christian himself, works and actively researches in the field of biology and evolution, writing peer reviewed research for a living, and has done so for quite a few decades. For a creationist to tell him he should read up on the facts is like trying to pass off a muppet as being a living biological being. I don't need to explain anything here.

EDIT: @pat34lee - I'll submit as my "proof, links and/or quotes" sfs' post below, is that sufficient enough for you?

 

[sfs]

She came up with pixie dust, I mean iron. Not even a decent fairy tale.
Keeping something for 2 years does not prove anything about eons.

Maybe she's wrong, but she's the world's leading expert on dinosaur soft tissue. She doesn't think that her findings undercut evolution. As a counterpoint, we have your statement that she's wrong, based on no evidence and no stated expertise in paleontology or chemistry. What you expressed wasn't a fact: it was an opinion, and (it seems) an opinion without any solid basis.

On ENCODE, the study that provides probably the best estimate to date of the fraction of the human genome that could actually contribute deleterious mutations is this one, which yields an estimate of about 10%. This alone is sufficient to demonstrate that your "fact" about ENCODE was not correct. There is also, however, reason to think that even that value is an overestimate: see this study.

Should we return to your claim about bacterial genes that are identical to human genes?

Ever actually looked up studies on mutations?

Yes, I've read a few studies on mutation. Here are some studies that include evidence for beneficial mutations in humans: here is one I've read, and here is another, and another and another and another and another. In fact, not only have I read all of those; I helped write all of them too. Beneficial mutations occur in humans. Now that is a fact.

 

[sfs]

@sfs, a Christian himself, works and actively researches in the field of biology and evolution for a living, and has done so for quite a few decades.

Slow down there a bit. It's two decades -- just two. (18 years, actually.) Let's not get ahead of ourselves in the aging process. Especially since I was a physicist for 10 years before becoming a geneticist.

 

[Bugeyedcreepy]

Slow down there a bit. It's two decades -- just two. (18 years, actually.) Let's not get ahead of ourselves in the aging process. Especially since I was a physicist for 10 years before becoming a geneticist.

Sorry, I knew you'd spent at least a couple of decades in various fields of Science and around 20 in genetics specifically and I guess I extrapolated to my imagination's satisfaction - so I stand corrected... I didn't mean to insinuate you to be older than you are, of course...

 

[Subduction Zone]

Previous refutations also refuted.

Nope, you have never done so.

 

[pat34lee]

Maybe she's wrong, but she's the world's leading expert on dinosaur soft tissue. She doesn't think that her findings undercut evolution. As a counterpoint, we have your statement that she's wrong, based on no evidence and no stated expertise in paleontology or chemistry. What you expressed wasn't a fact: it was an opinion, and (it seems) an opinion without any solid basis.

On ENCODE, the study that provides probably the best estimate to date of the fraction of the human genome that could actually contribute deleterious mutations is this one, which yields an estimate of about 10%. This alone is sufficient to demonstrate that your "fact" about ENCODE was not correct. There is also, however, reason to think that even that value is an overestimate: see this study.

Should we return to your claim about bacterial genes that are identical to human genes?

Last point first. Post #115, nothing about human there. No problem, it's easy to
mix up details unless you go back to recheck.
Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes | Molecular Biology and Evolution | Oxford Academic

Back to the first. Funny how -no one- ever considered iron as a preservative until the
soft tissue was found where it was impossible to be. They panicked and grabbed the
first halfway sane sounding excuse. Environmental factors could be counted out. Too
many different areas and times involved. It had to be something about the dinosaurs
themselves, because otherwise, they just couldn't be that old. Can't have that getting
around. The first thing real scientists should have done when she announced her
findings would have been to test them and challenge her. They didn't.

"Of course, if you understand the study, you recognize that the press has completely mangled the science. While the study represents an excellent first step in understanding how soft tissue can be found in fossils, it doesn’t solve the mystery of how it could be preserved for millions of years.

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

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

 

[pat34lee]

Nope, you have never done so.

Not personally, at least here, and neither have you refuted mine.

 

[pat34lee]

sfs, how does telegony affect the science of genetics?
https://www.sciencedaily.com/releases/2014/10/141001090238.htm

Telegony, the Sire Effect and non‐Mendelian Inheritance Mediated by Spermatozoa: A Historical Overview and Modern Mechanistic Speculations

 

[pat34lee]

JUNK DNA

"Vogel speculated that a lot of the genome was made up of essential noncoding DNA — possibly operating as something like switches, for example, to turn genes on and off. But other scientists recognized that even this idea couldn’t make sense mathematically. On average, each baby is born with roughly 100 new mutations. If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct.

Faced with this paradox, Crick and other scientists developed a new vision of the genome during the 1970s. Instead of being overwhelmingly packed with coding DNA, the genome was made up mostly of noncoding DNA. And, what’s more, most of that noncoding DNA was junk — that is, pieces of DNA that do nothing for us."
Is Most of Our DNA Garbage?

The Case for Junk DNA

 

[lesliedellow]

ROFLOL! Part there in bold italics - Does he even know he's talking to @sfs??

We all know somebody on here who thinks he knows more about astrophysics than all the world's astrophysicists put together, so why shouldn't pat34lee know more about biology than a lowly Harvard biologist?

 

[FrumiousBandersnatch]

Last point first. Post #115, nothing about human there. No problem, it's easy to
mix up details unless you go back to recheck.
Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes | Molecular Biology and Evolution | Oxford Academic

"As it stands, our present molecular work can neither confirm nor disprove the age of isolate 2-9-3."​

Funny how -no one- ever considered iron as a preservative until the
soft tissue was found where it was impossible to be. They panicked and grabbed the
first halfway sane sounding excuse.

Science progresses by making novel or unexpected discoveries and trying to find explanations for them. If you read the Royal Society paper on it, you'll find that 'exceptional' preservation isn't anything new, but this was much the best that had been found, and justified trying to find an explanation - which they did. The 'Discussion' section gives a very readable account of the whole business.

​

 

[Subduction Zone]

Not personally, at least here, and neither have you refuted mine.

Not true at all. I don't keep a list, but go ahead and make a claim.

 

[Gene2memE]

I gave a list of facts. Asserting that they are facts not doesn't change them.

Note: Second fact should have been dino soft tissue, not DNA.
That was carried over from fact one.

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

Otherwise, the harmful 99% of mutations build up and cause genetic failures
and ultimately, extinction.

Of course, some began creating new stories when ENCODE's work was published.
You cannot falsify a theory that transforms to fit any new facts.

The quote is pure human dangly parts - in fact it's worse. It shows either zero comprehension of the subject at hand and the original study, self-deception or and attempt to deceive the reader.

Here's the relevant passage from the original 2011 study

Avida
An experiment with Avida begins by seeding a two-dimensional grid with a short computer program (the ancestral organism) that has been designed to self-replicate. By default, a 60 × 60 grid is seeded with a single Avidian organism that consists of 100 computational instructions. This artificial geography allows the population to grow to a maximum of 3,600 organisms. Avidians replicate asexually for approximately 10,000 generations, incurring an average of 0.85 mutations per genome per generation. Mutations randomly substitute, insert, or delete single instructions in an Avidian genome, drawing upon 26 available instructions defined in the software. The ancestral genome devotes about 15 instructions to the essential replication code, while the remaining 85 positions are occupied by benign no-operation instructions, analogous to inert "junk DNA" that can be used as raw material for evolutionary tinkering.​

Notice there is nothing about REQUIRING the starting genome to have a certain percentage of junk DNA. The users of Avida can choose themselves how much/little 'junk' DNA is in the code in fitness studies. More available code, even non operational code, has both positive and negative fitness effects - in this case an overall positive, as larger genomes are artificially rewarded in the fitness landscape:

speed of replication in Avida is influenced by genome size. Organisms with larger genomes naturally require more computer time and replicate at a slightly slower rate. However, under default settings, this factor is offset by artificially rewarding larger genomes with additional computer time, such that genome size is not under direct selection in most experiments.​

I checked the Avida manual to be sure - there's no requirement for non-operational instructions for initial 'organisms' in the code at all. The only reference to non-operational code in the manual is on page 15:

In Avida, the default method is to select the minimum of executed and copied size to determine base merit. The relative value of the different methods is briefly discussed above. These different choices allow for a varying amount of junk (i e unexecuted or even uncopied to develop in the creatures genome).​

 

[pat34lee]

We all know somebody on here who thinks he knows more about astrophysics than all the world's astrophysicists put together, so why shouldn't pat34lee know more about biology than a lowly Harvard biologist?

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.

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

 

[pat34lee]

Notice there is nothing about REQUIRING the starting genome to have a certain percentage of junk DNA. The users of Avida can choose themselves how much/little 'junk' DNA is in the code in fitness studies. More available code, even non operational code, has both positive and negative fitness effects - in this case an overall positive, as larger genomes are artificially rewarded in the fitness landscape:

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.

 

[pat34lee]

"As it stands, our present molecular work can neither confirm nor disprove the age of isolate 2-9-3."​

Science progresses by making novel or unexpected discoveries and trying to find explanations for them. If you read the Royal Society paper on it, you'll find that 'exceptional' preservation isn't anything new, but this was much the best that had been found, and justified trying to find an explanation - which they did. The 'Discussion' section gives a very readable account of the whole business.

​

What can the present molecular work confirm about the age?

Does a two year experiment mean anything compared to
thousands, much less millions of years?

 

[lesliedellow]

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.

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

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.

 

[FrumiousBandersnatch]

What can the present molecular work confirm about the age?

Not very much, it would seem.

Does a two year experiment mean anything compared to
thousands, much less millions of years?

I guess it's possible to make a ballpark extrapolation to the very long term once you know the reactions involved, their rates, and the binding strengths of the reaction products, etc. The error bars will depend on environmental conditions - temperature, pressure, oxidants, etc., but much of that can be gleaned from the surrounding geology.