Evolution of de novo genes; a further nail in the coffin of intelligent design?

[FrumiousBandersnatch]

Hopefully each link tests the same story about "Junk DNA" and how it was the consensus.

In science, the consensus at any time is generally based on the best understanding and/or model of the available data. When reliable new data or better models or better understanding come along that challenge the consensus, it changes.

Can you suggest a more productive way of proceeding?

 

[Speedwell]

Here is a modern version of ignorance:
At least 75 per cent of our DNA really is useless junk after all


And here are the historical facts of matters:

With no obvious function, the noncoding portion of a genome was declared useless or sometimes called "selfish DNA," existing only for itself without contributing to an organism's fitness. In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.

Typically these sections of junk DNA come about through transposition, or movement of sections of DNA to different positions in the genome. As a result, most of these regions contain multiple copies of transposons, which are sequences that literally copy or cut themselves out of one part of the genome and reinsert themselves somewhere else.

Elements that use copying mechanisms to move around the genome increase the amount of genetic material. In the case of "cut and paste" elements, the process is slower and more complicated, and involves DNA repair machinery. Nevertheless, if transposon activity happens in cells that give rise to either eggs or sperm, these genes have a good chance of integrating into a population and increasing the size of the host genome.

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures.

What is junk DNA, and what is it worth?


It's all about how scientists are, in general, a herd of moo-cows that run whatever direction they think they will be feed fodder.

I don't see anything in there but an expression of the best understanding of the situation at the time. There is nothing like "denial," which is the rejection of a competent contrary opinion.

 

[Ophiolite]

I don't see anything in there but an expression of the best understanding of the situation at the time. There is nothing like "denial," which is the rejection of a competent contrary opinion.

It seems to be the ever recurring problem of "Look science was wrong before, so what science says now is also wrong, so we cannot trust science. (It's all lies.)"
I attribute it to a basic pyschological division between those who are comfortable with (or at least accepting of) uncetainty and those who require unshakeable and unchanging "facts".

 

[FrumiousBandersnatch]

It seems to be the ever recurring problem of "Look science was wrong before, so what science says now is also wrong, so we cannot trust science. (It's all lies.)"
I attribute it to a basic pyschological division between those who are comfortable with (or at least accepting of) uncetainty and those who require unshakeable and unchanging "facts".

I did occur to me that, just as we all have a tendency to be loss-aversive but some are able to overcome it by rationalising a loss of one sort as a gain of another (e.g. learning a useful lesson, or the good feeling of altruism), so we all have a tendency to be uncomfortable with uncertainty and prefer the certainty of belief, but some, e.g. good scientists, can rationalise the acceptance of uncertainty by cultivating a compensating certainty (belief, even) - that our knowledge of the world is inevitably uncertain.

 

[sesquiterpene]

Here is a modern version of ignorance:
At least 75 per cent of our DNA really is useless junk after all


And here are the historical facts of matters:

With no obvious function, the noncoding portion of a genome was declared useless or sometimes called "selfish DNA," existing only for itself without contributing to an organism's fitness. In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.

Except your "facts" aren't facts. Prof. Larry Moran has long argued against a few biologists (and many creationists) who don't quite understand the "junk DNA" debate:

There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago.

Sandwalk: Brandeis professor demonstrates his ignorance about junk DNA
And in an article in the journal PLOS entitled "The case for junk DNA", Alexander F. Palazzo and T. Ryan Gregory state:

It has now become something of a cliché to begin both media stories and journal articles with the simplistic claim that most or all noncoding DNA was “long dismissed as useless junk.” The implication, of course, is that current research is revealing function in much of the supposed junk that was unwisely ignored as biologically uninteresting by past investigators. Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently.

and

Importantly, the concept of junk DNA was not based on ignorance about genomes. On the contrary, the term reflected known details about genome size variability, the mechanism of gene duplication and mutational degradation, and population genetics theory. Moreover, each of these observations and theoretical considerations remains valid.

The Case for Junk DNA

Finally, Prof Moran insists that pretty much that all knowledgeable scientists still realize that >75% of the genome is junk.
Sandwalk: Five Things You Should Know if You Want to Participate in the Junk DNA Debate

 

[Subduction Zone]

There is no such thing as natural means. Nothing in the Cosmos is random.

Really? Do you have any evidence for that?

 

[Subduction Zone]

Hopefully each link tests the same story about "Junk DNA" and how it was the consensus.

"Junk DNA" is just the result of evolution. There are specific genes that no longer work that can be identified as "Junk DNA". From your posts it appears that you are at least admitting that man is a product of evolution.

 

[xianghua]

And in an article in the journal PLOS

if this is indeed junk then how you explain the correlation between creature complelxity and the amount of junk in general?:

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%D7%AA%D7%9E%D7%95%D7%A0%D7%94760×350 95.9 KB
(image from A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI 4)

 

[FrumiousBandersnatch]

if this is indeed junk then how you explain the correlation between creature complelxity and the amount of junk in general?:

%D7%AA%D7%9E%D7%95%D7%A0%D7%94787×762 87.7 KB


%D7%AA%D7%9E%D7%95%D7%A0%D7%94760×350 95.9 KB
(image from A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI 4)

It would not surprise me if we continue to discover more 'junk' that is functional - but I don't see how the speculation in this paper, that "ncDNA, and the ncRNAs encoded within it, may be intimately involved in the evolution, maintenance and development of complex life", helps your case against evolution.

 

[The IbanezerScrooge]

Did I ever mention that people invent their own reality no matter what others can see?

My irony meter just broke!

 

[Oncedeceived]

One of the cornerstones of the intelligent design argument is that natural processes are incapable of creating the necessary genetic information to enable the various functions required for biological organisms.

Stephen Meyer (currently the most prolific ID proponent) in particular makes this a crux of his core argument for ID. He uses it in particular in the context of the Cambrian explosion, claiming that evolution cannot explain the origin of all the required genetic information for Cambrian fauna.

Lately I've been reading up on the concept of de novo gene evolution. Traditional thinking of the evolution of genes revolves largely around gene duplications and subsequent evolutionary modification. IOW, new genes evolving from pre-existing genes.

With de novo gene evolution, you have the evolution of new genes from non-genic DNA. In this manner, novel genes can evolve without ancestral genes preceding them.

This paper in particular describes various proposed mechanisms for de novo gene evolution: De novo gene birth

This area of gene evolution appears less understood, but as more is learned about how de novo genes evolve, that can further answer the question of where all that wonderful genetic information came from.

Actually Stephen Meyer is not just centering his argumentation on the Cambrian. The point here is that the information found later does nothing to explain how information arose in the first place.

 

[pitabread]

The point here is that the information found later do nothing to explain how information arose in the first place.

We already have an explanation for how genetic information arises: evolution.

 

[Oncedeceived]

We already have an explanation for how genetic information arises: evolution.

No, evolution can not happen until the information is there first.

 

[Speedwell]

No, evolution can not happen until the information is there first.

Enough information to produce a simple, self replicating life form so that the evolutionary process itself could begin to produce more. Where that initial information came from is the subject of a separate field of scientific study called abiogenesis.

 

[Oncedeceived]

Enough information to produce a simple, self replicating life form so that the evolutionary process itself could begin to produce more. Where that initial information came from is the subject of a separate field of scientific study called abiogenesis.

Yes, true. However, abiogenesis is necessary for life to exist and then evolve. Editing to add: a self-replicating isn't life until information can be conveyed.

 

[Speedwell]

Yes, true. However, abiogenesis is necessary for life to exist and then evolve. Editing to add: a self-replicating isn't life until information can be conveyed.

So you should be criticizing abiogenesis instead of evolution. The theory of evolution is pretty solid and well-evidenced but there is not, at this point, even a coherent theory of abiogenesis.

 

[pitabread]

No, evolution can not happen until the information is there first.

By any definition of "information" that is directly applicable to genetics, evolution can and does give rise to said information.

Which is the entire point of this thread: mechanisms by which de novo genes can arise via evolution.

If one wishes to argue otherwise (e.g. that there is some sort of nebulous"information" in biology by which evolution cannot account for), then that needs to be demonstrated. Thus far, I have not seen any support for such claims. And yes, I've read the ID literature on the subject and already know exactly why such claims are inherently flawed.

 

[pitabread]

Yes, true. However, abiogenesis is necessary for life to exist and then evolve. Editing to add: a self-replicating isn't life until information can be conveyed.

My reference to Meyer's claims in the OP has nothing to do with abiogenesis. Meyer's claims in his latest book are specific to the Cambrian explosion which occurred about ~3.5 billion years after life arose on Earth.

Abiogenesis is a red herring in this discussion.

 

[Oncedeceived]

So you should be criticizing abiogenesis instead of evolution. The theory of evolution is pretty solid and well-evidenced but there is not, at this point, even a coherent theory of abiogenesis.

You claimed there was enough information for a self-replicating module but that isn't the case. Pitabread claimed that evolution was how information arose, I was commenting on that.

 

[Oncedeceived]

By any definition of "information" that is directly applicable to genetics, evolution can and does give rise to said information.

Which is the entire point of this thread: mechanisms by which de novo genes can arise via evolution.

If one wishes to argue otherwise (e.g. that there is some sort of nebulous"information" in biology by which evolution cannot account for), then that needs to be demonstrated. Thus far, I have not seen any support for such claims. And yes, I've read the ID literature on the subject and already know exactly why such claims are inherently flawed.

I stand corrected on the thread subject. I will address this post since you responded.

Can you demonstrate how information arose without any evolution taking place? I am not claiming that information isn't passed on through evolutionary processes but I am referring to where information arose in the first place.