The Limits of Evolutionary Optimization

a reply to: deliberator

So what exactly is the point of your thread, then? To spread creationist propaganda? Because that's what you're doing.

So I am deliberately spreading creationist propaganda on top of your other allegations?

The research claims to disprove the promiscuity and junk hypotheses in relation to specific proteins. I am not sure if this is universally relevant. There are knowledgeable people on ATS who may be able to answer that question or show its relevance.

You consider this propaganda? I thought it was intellectually inviting. Is it not the ethos of ATS to present information, views or ideas to promote constructive discussion? So by your reckoning people should be policed on what they read and judged if they stray?

In retrospect I should have checked the validity of the journal. This was pointed out to me and I acknowledged this. I was interested in the study. spygeek and chr0naut and Barcs took the time to answer my questions which allowed me to make an informed opinion. I thought it was valid and they showed me it was not.

Why is this an agenda? How on earth have you come to the conclusion that I am promoting creationism?

a reply to: deliberator

Yes, you are deliberately spreading creationist propaganda on top of my other claims.

Either that or you're the world's worst postgraduate who cannot differentiate between a legitimate academic source and blatant creationist propaganda.

What's your agenda here?

The world's worst? pmsl Your really want me to respond to infant talk?

I have tried to reason with you. Your intention is now clear. This is nothing more than a feeble attempt to troll.

originally posted by: GetHyped
a reply to: deliberator

Yes, you are deliberately spreading creationist propaganda on top of my other claims.

Either that or you're the world's worst postgraduate who cannot differentiate between a legitimate academic source and blatant creationist propaganda.

What's your agenda here?

i think you're being a bit unfair here gethyped.. i usually enjoy your posts but in this thread you seem to be more focused on belittling the op than actually discussing the topic.. deliberator has already admitted not doing his background research on the scientists and the institute involved, and to being duped by the apparently scientific presentation of this "research", clearly he is not "deliberately spreading creationist propaganda".

the op wanted us to help him understand this "research" and answer the question of its relevance, nowhere did he state that he categorically accepted it. the whole point of sharing creationist studies like these is to assess them for relevance and quality.

originally posted by: deliberator
a reply to: spygeek

Hi spygeek. I really appreciate your critique and taking the time to post with links. I understand its relevance now and also the intellectual dishonesty of the authors. I am actually agnostic and like to read on both sides of the argument although some of it is too complex for me to understand. It appeared to me that it was legitimate research but you have shown it is not.

Thank you. People like you are an asset to ATS.

my pleasure. i have seen many studies like these and without exception they have been inadequate to substantiate the inferences claimed. it is important to have these studies put out there to be dissected and evaluated, as they prey on the laypersons' lack of scientific knowledge. these studies are indeed propaganda dressed up as legitimate study, and i thank you for sharing this new one so it may be identified as such.

too many people fall into the trap of accepting the supposed findings of any study that uses scientific jargon and apparent method, when it is in fact not scientific at all. threads like these are invaluable for people who might otherwise hold findings like these in high regard and spread the dishonesty, so again, thank you for sharing this and helping us all deny such ignorance.

originally posted by: deliberator
The world's worst? pmsl Your really want me to respond to infant talk?

I have tried to reason with you. Your intention is now clear. This is nothing more than a feeble attempt to troll.

I have been called a creationist on ATS before, too.

It would appear that if you even so much as suggest that there may be a possibility of an alternate to evolutionary dogma (and there is much that is not religious - i.e: epigenetics, panspermia, catastrophism, ancient aliens, the idea that abiogenesis occurred many times and not once - making the phylogenic tree a nonsense and saltationism to name a few), you are labelled as such.

I suspect that it is actually more telling about the personality of the name caller, so I wouldn't sweat it.

As this paper draws conclusions that far overreach its very specific and limited results, I also find that some papers that are in agreement with evolution do exactly the same thing, even though they are "peer reviewed". Often a pre-existent paradigm can drive the most educated into making false assumptions.

That you questioned the paper shows a strong degree of comprehension and curiosity. I personally applaud that.

Cheers!

a reply to: spygeek

Yes I was duped. It was the mention of the b-lactamase enzyme which gave me a false sense of credibility. Forewarned is forearmed.

originally posted by: deliberator
a reply to: spygeek

Yes I was duped. It was the mention of the b-lactamase enzyme which gave me a false sense of credibility. Forewarned is forearmed.

I implore you to not be ashamed or embarrassed by this, it happens to pretty much everyone, myself (and gethyped, i would wager) included. Don't let the ad hominem attacks discourage you from sharing such things in future, education against ignorance is more important than an individual ego.

a reply to: chr0naut

I try to keep an open mind on the origins of existence although I rely on science regarding the theory of evolution. When I mentioned the evolution hypothesis in a previous post to spygeek I was actually referring to science which tries to explain the origins of existence eg multiverses (on the net this is referred to as evolution hypothesis). It should be have a separate name to avoid confusion (maybe it does and I am not aware of it).

a reply to: spygeek

Thanks for the reassurance. I enjoyed reading your thread on fallibility last night.

originally posted by: deliberator
A recently published research article from the Biologic Institute, Redmond, Washington, USA (funded by the Discovery Institute).

Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention—Selection Itself Is Not Inventive

Since biological inventions only benefit their possessors after they work, their origins cannot be attributed to their selective effects. One proposed solution to this conundrum is that selection perfects activities that already existed in rudimentary form before they became beneficial. An example of this idea for protein origins is the promiscuity hypothesis, which claims that minor aberrant side-reactions in enzymes can be evolutionary starting points for proficient new enzymes. Another example—the junk hypothesis—claims that proteins arising from accidental expression of non-genic DNA may likewise have slight activities that, through evolutionary optimization, lead to proficient enzymes.

Here, we tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor. The extreme weakness of the original activities, however, meant even large improvements could be inconsequential. Indeed, the endpoint was itself a proficient design only in the case where this design was largely present from the outset.

Laboratory optimization of ampicillin-resistance proteins derived from a natural β -lactamase produced similar results. Our junk protein here was a deletion mutant that some - how confers weak resistance without the original catalytic mechanism (much of the active site having been lost). Evolutionary optimization was unable to improve that mutant. In contrast, a comparably weak mutant that retained the active site surpassed the natural β -lactamase after six rounds of selection. So, while mutation and selection can improve the proficiency of good designs through small structural adjustments, they seem unable to convert fortuitous selectable activities into good designs.

Link to Research Article

There is also a podcast from the Discovery Institute.

Andrew McDiarmid talks to Dr. Ann Gauger, a senior research scientist at Biologic Institute and co-author with Dr. Douglas Axe of a new paper recently published in the journal BIO-COMPLEXITY that probes the limits of evolutionary optimization. Gauger explains how she and Axe tested popular hypotheses for protein origins and discovered that while mutation and selection can improve the proficiency of good designs through small adjustments, they seem unable to convert fortuitous selectable activities into good designs.

Podcast Link

I think the mere sight of the words "Discovery Institute" may annoy some and promote vociferous posts although I am more interested in the study. The research claims to disprove the promiscuity and junk hypotheses in relation to specific proteins. I am not sure if this is universally relevant. There are knowledgeable people on ATS who may be able to answer that question or show its relevance.

IDC is often referred to as being supported by pseudo-science which is also inherently biased. This research is certainly not pseudo-science. Is the testing of evolution hypothesis, as is done here, biased? I am inclined to think it is not.

Considering evolution is merely a process that explains biodiversity and there is no such thing as optimizing involved, this premise fails in the title alone. (in other words mutations can be both beneficial or a detriment pending the environment). All a mutation needs to get passed on is for an organism to survive long enough to pass that gene on. The optimal argument is a fallacy. That is why it is not going to be taken seriously.