The Limits of Evolutionary Optimization

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.

Prepare to be smashed by atheists who hate the idea that diencephalic should be questioned

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.

More pseudo-scientific bollocks by creationists pretending to be scientists.

a reply to: Raggedyman

Only creationist cultists equate modern evolutionary synthesis with atheism because they want to frame it as a religion vs atheism argument rather than the sorry fact that they're an extremist minority of religious folk.

As I said in my OP I expected some vociferous posts. What I am actually looking for is constructive critique of the research.

a reply to: deliberator

Yeah, you already mentioned it at the bottom, but this was funded by the Discovery Institute. Huge red flag. They don't do science over there. They are a Christian apologist group.

About the "journal" it was published in:

rationalwiki.org...

BIO-Complexity is (or, perhaps more properly, was) an open access journal published by the Biologic Institute. The journal "aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life."[1]

The first two articles[2][3] exploit ambiguities in biochemical mechanisms in the typical "God of the gaps"-type argument, and neither provides evidence for an intelligent designer; neither even mentions a designer in the paper.[4] Both articles have authors from the Biologic Institute's editorial board[5] (which also includes ID leaders William Dembski and Michael Behe). The Discovery Institute lauded the journal's formation, implying that intelligent design papers were ideologically blocked from publication.[6]

About the institute that does the research:

rationalwiki.org...

The Biologic Institute is a Creation science group dedicated to verifying intelligent design through pseudoscientific research. It is a non-profit group funded and staffed by the Discovery Institute. The concept was first developed as part of the wedge strategy which called for Douglas Axe to create an organization to do intelligent design research. In 2005 Axe created the Biologic Institute.

Published research

In 2008, the Biologic Institute published its first "research" in the open access journal PLoS ONE. The paper introduces a computational model for protein simulation call Stylus. The program creates 2d protein structures out of amino acids coded by genes and then compares these to Han Chinese characters.
What?

Since the Han characters have a function that emerges from their structure the paper argues this is a computationally efficient analogy to real life proteins. [7]

The paper makes no claims in regards to evolution or intelligent design. It is merely a description and publication of protein modeling software. In a press release about the research the Biologic Institutes claims that it might eventually be able to use this simulation to show the "edge of evolution" but admits that they might wind up showing the power of evolution instead. [8]

In 2010, the institute started its own journal, BIO-Complexity.

This is how they do "science" there. They start with the conclusion and work backwards. The conclusions themselves are downright ridiculous and have no connections to any physical real world data.

I knew as soon as I read the title that it was going to be pseudoscience that does nothing at all to suggest intelligent design OR refute evolution. The limits of evolutionary optimization? That's pretty much technobabble. Can genes mutate in random places? Are any genes off limits from coding changes caused by them? The only limitation is in their computer software. Software does not physically alter the machine that it runs on, so any comparison to real evolution limitations is completely baseless.

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.

It's all based on a computer program, not even hard data with real amino acids and proteins. It is HUGELY flawed, as it does not factor in natural selection (or natural anything really). Maybe not technically pseudoscience, but certainly not applicable science to what they are claiming.

Evolution is a THEORY, not a hypothesis. Hypotheses are unproven "educated guesses" based on data to explain something. Theories are well backed and well substantiated explanation of a verified phenomenon.

Sorry about the million and one edits. Trying to keep it thorough.

a reply to: deliberator

Although the paper does seem to make a valid point, philosophically, I would think that computer simulations and observed adaptation in populations argue strongly against what the paper proposes.

The paper is splitting hairs and looking at evolutionary mechanics as if each 'component' existed in isolation. The thing is that the forces involved work at the same time as well as in a nice procedural sequence. Everything overlaps, chaotically.

Of course natural selection cannot explain an instance of a new trait, but mutation, genetic drift and such as epigenetics, do. Subsequent to these, "optimization" can occur by methods such as natural selection, but may also include forces such as organism behavior and simple random chance (remember we are speaking of populations of living organisms, therefore statistical results can be significant).

The language of the paper is mind-numbingly convoluted, too, so I think most will give up on trying to critique it. It could have said things with greater clarity and brevity (IMHO).

I DO think we need to 'open' old ideas of evolution to newer mechanisms, redefining our reductionist definitions and allowing a multiplicity of mechanisms and how they interrelate to produce the biological change that we now observe.

originally posted by: deliberator
As I said in my OP I expected some vociferous posts. What I am actually looking for is constructive critique of the research.

Here you go:

This uninformed "research" does not show any extent of limitation of "evolutionary optimisation" at all. If anything it shows the limitation of these creationist scientists' ability to design and perform a meaningful experiment. It also ignores previous experiments that have already shown that the results of this experiment are to be expected and fit with evolutionary theory.

"Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention—Selection Itself Is Not Inventive". Well, duh. This is accepted and is not controversial, let alone a "conundrum" as claimed.

What this experiment does is attempt to reproduce a chosen evolutionary pathway from an arbitrarily chosen starting point, which it then fails to do. It is then wrongfully asserted that this failure proves that it is not possible for this chosen pathway to have occurred through natural selection. The problems with this experiment include the fact that it only observes six "rounds of selection", (generations, or what?), and that the experimenters themselves do not even know which proteins they were adding.

Furthermore, this experiment's strategy essentially constitutes a "replaying of life's tape", which is not a practical means to make any kind of judgement on the limitation of evolutionary mutation and natural selection other than it's inherent unpredictability. As Stephen Jay Gould puts it:

I call this experiment 'replaying life's tape'. You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past--say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to happen. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self conscious intelligence? Or of mammals? Or of life on land? Or simply of multicellular persistence for 600 million difficult years?

The fact is that the "tape of life" would produce very different results each time it is replayed has already been well demonstrated and universally accepted. The most well known experiement showing this is Richard Lenski's long term, (as in, 20 years long!) E. coli experiment.

All these creationist buffoons, Douglas Axe and Ann Gauger, have done is further confirming the finding that random mutations are random and largely unpredictable. You will not get the exact same results every time you do an experiment involving random processes. History does not repeat itself exactly every time.

Ironically, this experiments by devoted creationists have rather clearly and neatly proven evolution; they have apparently facilitated the creation of an antibiotic resistant superbug through completely undesigned natural processes, no intelligent design required.

These experimenters have made the rather plebeian failure of making an inference that is not supported by their experiment, and they have rather counter-productively proven the opposite; that natural selection in fact can facilitate the improvement and solidification of beneficial genetic traits.

It might be worth also mentioning that Douglas Axe has a bit of habit of doing this. He will perform an experiment that produces reults that fit with evolutionary predictions, and then claim that it in fact disproves the theory. Like this, and this. He is not, by any definition, an honest, competent and knowledgeable scientist. He, like most creationists, also likes to use the false dichotomy fallacy to prop up his arguments for creationism, like this.

Ann Gauger is guilty of similar intellectual dishonesty. I would take anything her and Douglas assert with a massive grain of salt.

a reply to: deliberator

By "research", you mean creationist propaganda?

Notice that this sort of "let's play science" baloney isn't actually meant to convince normal, rational people. It's not supposed to try and convince normal religious folk and atheists alike. It's simply propaganda for the True Believers to ease their nagging doubts that all those claims from the pulpit don't quite jive with the modern understanding of the world.

If you want "constructive critique of the research", you can start by posting up some actual scientific research.

a reply to: GetHyped

Notice that this sort of "let's play science" baloney isn't actually meant to convince normal, rational people.

For someone who posted the OP to actually learn something you have not really contributed have you?

I am a normal intelligent person with post graduate education and I could not understand parts of it. So that makes me less than normal and also religious apparently. Interesting.

Thanks for taking the time to post guys. It is getting late here so will answer them tomorrow. Thanks for the links as well Barcs.

a reply to: deliberator

If you're a postgrad then you would know what a credible academic source is. A creationist propaganda outfit is not.

And this may come as a surprise to you but normal, rational people do not take the literal interpretation of their holy text's creation myth over rigorous, scientific evidence. Thus, I hate to break this to you, but you are not a normal, rational person.

a reply to: Barcs

Hi Barcs. To be honest it is the first time I have link-hopped onto the Discovery Institute website so was not aware that they effectively employ the scientists. Thanks for the background info.

a reply to: chr0naut

Hi chr0naut. Thanks for the review. I did wonder if replicating a few cycles is comparable to evolution over thousands of years. I did not state this as I am not knowledgeable on the subject and also the fact that there are certain members who do not appreciate that you are trying to acquire knowledge an instead belittle you.

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.

a reply to: GetHyped

????? I am not religious! If you think Joe Public can interpret and understand what is being said then it only shows arrogance. Looking at your recent posts on other threads you never contribute, just attack.

If you really have that knowledge why not be constructive and share like the others have done. If not then why bother to post?

a reply to: deliberator

You are quoting creationist propaganda. You are either being dishonest or profoundly mistaken.

And no, it is not an "ad hominem" to point out the fact that normal, rational people do not believe that the world is 6k-10k years old and that life was created as-is by a supreme being, eschewing the mountain of scientific evidence that says otherwise.

What is your agenda here?

a reply to: GetHyped

I changed my post while you were posting. I have no agenda. I think the above makes it very clear.

a reply to: deliberator

For the last time:

Bio-Complexity is not an academic journal. It's a creationist propaganda publication.

The Discovery institute is not an academic institutio. It's a creationist propaganda organisation.

You say "I'm not a creationist!" yet you are parroting creationist propaganda.

What is your agenda here?

a reply to: GetHyped

The other posters answered my questions. Why do you feel the need to repeat what has already been discussed in detail and to also write "for the last time" which is condescending, arrogant and also misleading. You assume that I am a creationist and have ignored all the posts. Presumptuous and not based on anything real.

Please do not make up things I did not say and try to manipulate my intention. Your claims that I am "parroting creationist propaganda" has no substance, has nothing to do with the thread and is therefore irrelevant. A reasonable intelligent person can see from my posts that I have no agenda, just an inquisitive mind.

To state that all creationists are religious and all believe the world is 6000 years old shows a great lack of understanding on your part. Creationism does not exclude evolution from what I have read. I know this because I am inquisitive about both sides of the argument, but by your assumption, because I have read it I must believe in it 100%, be religious and also be educationally sub-normal and irrational.

I will not engage in "playground" mentality or one-upmanship. Sorry but it is pathetic.