Dispatches from the Creation Wars

There’s a very interesting post on the Newsweek blog by science journalist Sharon Begley about the existence of genes for synapses in the sea sponge, which has no need for such structures. Begley is discussing an article in PLoS One that found that the same genes that code for synapses are present in sea sponges, one of the most primitive multicellular organisms on the planet, which have no nervous system and therefore no need for synapses. Begley writes:

Considered among the most primitive and ancient of all animals, sea sponges have no nervous system (or internal organs of any kind, for that matter), notes Todd Oakley, assistant professor in the Department of Ecology, Evolution and Marine Biology at the University of California, Santa Barbara. But, he adds, they “have most of the genetic components of synapses.”…

He, Oakley and the rest of the team listed all the genes known to be operative in synapses in the human nervous system. They then examined the sponge genome. “That was when the surprise hit,” said Kosik. “We found a lot of genes to make a nervous system present in the sponge.”

Not only do sea sponges have the genes to produce synapses, many of those genes are absolutely identical to the same gene in humans, yet we did not evolve until more than 600 million years later. From the PLoS paper:

We show that the genome of the demosponge Amphimedon queenslandica possesses a nearly complete set of post-synaptic protein homologs whose conserved interaction motifs suggest assembly into a complex structure. In the critical synaptic scaffold gene, dlg, residues that make hydrogen bonds and van der Waals interactions with the PDZ ligand are 100% conserved between sponge and human, as is the motif organization of the scaffolds.

What does all this mean in terms of the dispute over evolution and intelligent design? Begley makes the (correct) argument that IDers ignore the ability of evolution to use already existing components with one function and adapt them for a new function, what Gould famously called exaptation:

What were genes for synapses doing in a sponge, which has no neurons and therefore no synapses? This is where the irreducible-complexity crowd makes a fatal error: they assume that whatever the function of a biological component (gene, protein, biochemical pathway . . . ) today must have been its function in the past. Maybe you noticed that my mouse trap example above wasn’t very persuasive; even without a base and a bar, a spring can be a useful little device. So it goes with biological systems. For instance, of the 42 proteins known to make up the bacterial flagellum, 40 have been found to serve as ion channels or something else in bacteria. It is therefore perfectly plausible that they really were hanging around–serving some function that would have allowed evolution and natural selection to keep them around generation after generation–until they all got together and formed a flagellum.

So it seems to be with the genes for synapses. The sea sponge did not use them for their current purpose, but that doesn’t mean the genes had no use. “We found this mysterious unknown structure in the sponge, and it is clear that evolution was able to take this entire structure and, with small modifications, direct its use toward a new function,” said Kosik. “Evolution can take these ‘off the shelf’ components and put them together in new and interesting ways.”

This is accurate as far as it goes, but there is much more to be said. What ID advocates would likely say in response to this finding is that it is an example of front loading rather than exaptation. Front loading is the idea that God (no, I’m not going to engage in the ridiculous fiction that the generic designer they posit is anything other than God) programmed in all of the genetic information necessary for later developments in to the first cell. Michael Behe famously proposed this in Darwin’s Black Box:

Suppose that nearly four billion years ago the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not “turned on.” In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)

So which is the best explanation for the existence of such genes in the sea sponge, exaptation or front loading? Le’ts look at what each explanation would predict. Back when Behe proposed this idea, Ken Miller pointed out the most obvious problem with it: runaway mutations. Natural selection can only work on genes that are expressed. If a gene is “turned off” then it is subject to runaway mutations that will render if useless in short order. Miller wrote:

This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic “cold storage.” And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

Quite right. But remember, some of those genes are highly conserved or 100% conserved – that is, identical or nearly identical – between sponges and humans. And while front loading means those genes had to be “turned off” for hundreds of millions of years, exaptation posits that those genes were turned on, expressed in the phenotype and serving different functions. Thus, exaptation is consistent with the preservation of those genes while front loading is not.

Equally as important, while front loading presumes that those genes serve no function before they are later expressed, exaptation predicts that they must have some function if they are highly preserved over a long period of time. They simply must be expressed in the phenotype for some function or they will mutate in to uselessness. And that is exactly the case here, as this study found that those genes, though virtually identical between sponges and humans, serve a different function in sponges than they do in humans (obviously so, since the sponges have no nervous system).

There are only two ways out of this for ID advocates: either they have to accept that those front-loaded genes had different functions in earlier species (which effectively makes front loading synonymous with exaptation, rendering the idea meaningless) or they have to posit that God not only loaded the genes for all those later developments in to earlier organisms that didn’t need them, but he also put some sort of mystical force field around them to prevent them from mutating over the last 4 billion years.

The other problem, of course, is that no one has ever found an organism that has all of the genes needed for later developments (feathers, wings, lungs, flagella, etc); that is, no organism actually has a fully complete genome front-loaded with all the goodies to be used later. If front loading was true, then the prokaryotes – the earliest existing life form on Earth – should have all of those genes. They don’t, of course. The bottom line is that the evolutionary hypothesis, exaptation, predicts the evidence perfectly; the ID hypothesis is flatly contradicted by it and can only try to explain it away or invent mystical and unknown processes to circumvent the evidence.

Comments

#1 Mikado
June 8, 2007

There are only two ways out of this for ID advocates: either they have to accept that those front-loaded genes had different functions in earlier species (which effectively makes front loading synonymous with exaptation, rendering the idea meaningless) or they have to posit that God not only loaded the genes for all those later developments in to earlier organisms that didn’t need them, but he also put some sort of mystical force field around them to prevent them from mutating over the last 4 billion years.

Or, invoke young earth creationism.
#2 Kevin Klein
June 8, 2007

I don’t see why ID’ers couldn’t simply say that not only did the designer front-load the genes for neurons, but he also was smart enough to front-load primitive functions for them to perform to protect them from mutational degradation.

Any time one tries to disprove ID that “nailing jelly to a tree” adage always comes to mind.
#3 carlsonjok
June 8, 2007

or they have to posit that God not only loaded the genes for all those later developments in to earlier organisms that didn’t need them, but he also put some sort of mystical force field around them to prevent them from mutating over the last 4 billion years.

Praise be to the Disembodied Telic Entity!!
#4 DougT
June 8, 2007

And while front loading means those genes had to be “turned off” for hundreds of millions of years, exaptation posits that those genes were turned on, expressed in the phenotype and serving different functions.

Not only is this a prediction of exaptation, it’s a *gasp* testable prediction. If exadaption hold, the genes should still be expressed in modern sponges and they should be playing some sort of function in them. Leading to another difference between ID and real science
#5 Brandon
June 8, 2007

an authoritative and enlightening scientific explanation of natural phenomena that will ultimately replace the Darwinian view

Is there any mention of bananas, coke cans, or peanut butter?
#6 J-Dog
June 8, 2007

Hey Linda Parsons – WOW! What a coincidence! The Lord just appeared to me in a vision last night, and he said you should bite me! Then he said that you will die of a horrible lingering disease that he created at an unspecified time in the future.

HTH
#7 Scott Reese
June 8, 2007

Author, C. David Parsons, biblical scholar and scientist extraordinare.

Wow! What does it take to be a ‘scientist extraordinare?’ I want to be one. I always thought the great scientists got nobel prizes or, at least, were in the National Academies, but I’ve never heard of David Parsons and he’s a ‘scientist extraordinare.’ Must be an awards committee I’m unfamiliar with, can I self-nominate?
#8 Scott Reese
June 8, 2007

ooooo, imagine my tenure portfolio with the title “Scott Reese, Scientist Extraordinare!” They’d be crazy to deny me tenure (or persecuting me for my evolutionistic stance).
#9 chris
June 8, 2007

I’m assuming Linda’s post is a jest, because it can’t possibly be real. Also, apparently God needs a spell checker:

Barnes and Nobel.com

What, Borders couldn’t agree to terms?
#10 chris
June 8, 2007

Also, it’s interesting that they both have the same last name. It seems bit of a conflict of interest for a scientist extraordinaire to have his wife/sister/mother/cousin/etc as his PR flak.
#11 EJ
June 8, 2007

“If front loading was true, then the prokaryotes – the earliest existing life form on Earth – should have all of those genes.”

Your claim seems to be based on a misconception. Certainly all multicellular life had some unicellular ancestor. But this does not mean that the prokaryotes of today are the same as that unicellular ancestor! Just like all other species, the prokaryotes that you see today have been for billions of years evolving (according to evolutionary theory) or perhaps devolving (according to front-loadary theory). Front-loadists would say that we *might* see that some prokaryotes have a lot of genes that have never been “switched-on”, but we wouldn’t necessarily. Don’t worry — a lot of YECs make the same mistake you did.
#12 Ed Brayton
June 8, 2007

Sorry guys, I deleted the spam comment from Linda Parsons. If she wants to come here and make an argument, that’s fine. If she wants to come here just to spam advertise their crackpot book, those will be deleted immediately.
#13 mark
June 8, 2007

If God shipped the original front-loaded unit out of the factory, why did not the function that was front-loaded, well, function? Gene regulation affects development and evolution, but do the Creationists mean evolution does occur, but it just involves gene regulation and not the genes themselves?

Perhaps someone else can explain this to me…maybe THE QUEST FOR RIGHT, a masterful work by a scholar and scientist extra hair, holds the key.
#14 chris
June 8, 2007

While I applaud the decision to delete spam, unfortunately now we all appear to be loonies!
#15 Ed Brayton
June 8, 2007

EJ wrote:

Your claim seems to be based on a misconception. Certainly all multicellular life had some unicellular ancestor. But this does not mean that the prokaryotes of today are the same as that unicellular ancestor! Just like all other species, the prokaryotes that you see today have been for billions of years evolving (according to evolutionary theory) or perhaps devolving (according to front-loadary theory). Front-loadists would say that we *might* see that some prokaryotes have a lot of genes that have never been “switched-on”, but we wouldn’t necessarily. Don’t worry — a lot of YECs make the same mistake you did.

This is all nonsense. The only way they can make this claim is if all of those genes magically disappeared from the genomes of all of the descendant species (and remember, the front loading hypothesis accepts common descent) after being expressed. And that is exactly the problem with the front loading explanation rather than the exaptation explanation – it requires multiple ancillary hypotheses to avoid the laws of nature (like protecting the unexpressed genes from runaway mutations, which we know happens in nature because we can observe it, and like positing some mechanism by which those frontloaded genes magically vanish from the genomes of the more primitive descendant species after they’re switched on in other species).
#16 mark
June 8, 2007

Can’t they claim that is accounted for by the “information can only be lost–never created” mantra? (This would assume that evolution has reached its final goal, all front-loaded “information” has been realized as intended.)
#17 Science Avenger
June 8, 2007

…or they have to posit that God not only loaded the genes for all those later developments in to earlier organisms that didn’t need them, but he also put some sort of mystical force field around them to prevent them from mutating over the last 4 billion years.

Which is exactly what they’ll do. They’ll invent a “loaded cohesiveness” to keep the front loaded genetic information from unravelling, just like they invented the “genetic limit” to keep microevolution from becoming macroevolution.

Once again we see the clear difference: scientists do science, IDers/creationists just make shit up.
#18 DuWayne
June 8, 2007

chris -

Good grief, what a pack of loonies! I see no comments from a Linda Parsons, you all must be crazy. . .
#19 CCP
June 8, 2007

Ed, excellent post. Interested parties ought to see the post and comments on this article over at Pharyngula.

One pedantic correction, but one which actually strengthens your case, I think:
“Not only do sea sponges have the genes to produce synapses, many of those genes are absolutely identical to the same gene in humans”
Actually, the passage quoted does not say that the genes are absolutely identical, but rather that only those residues (amino acids) that actually participate directly in binding the ligand are 100% conserved. No doubt there are many differences in the less critical parts of the sponge & human proteins.
#20 Nick (Matzke)
June 8, 2007

Wow…we’ll make an ubernerd out of you yet, Ed…
#21 Matt Brauer
June 8, 2007

Ed,

I think you’re too quick to dismiss EJ’s comment. Your post really does sound like a claim that modern prokaryotes = ancestral prokaryotes. By referring to bacteria, sponges and such as “more primitive descendant species” you invoke the Scala Natura.

As nutty of an idea as front-loading is, there’s nothing in it that requires modern prokaryotes to retain all of the genes of the original front-loaded ancestor.
#22 DuWayne
June 8, 2007

Mark -

If God shipped the original front-loaded unit out of the factory, why did not the function that was front-loaded, well, function? Gene regulation affects development and evolution, but do the Creationists mean evolution does occur, but it just involves gene regulation and not the genes themselves?

According to an OEC/ID friend of mine, this was God’s way of putting all the material to build people, into the physical, before actually creating us. She had a very long and detailed explanation for why God did it that way, but my brain shut down in self-defense and I missed most of it.

I think that this falls nicely with Science Avenger’s notion that they just make shit up. I am pretty sure she came up with it on the spot, when presented with an argument that the book on ID she had read didn’t cover.
#23 Ed Brayton
June 8, 2007

Matt Brauer wrote:

I think you’re too quick to dismiss EJ’s comment. Your post really does sound like a claim that modern prokaryotes = ancestral prokaryotes. By referring to bacteria, sponges and such as “more primitive descendant species” you invoke the Scala Natura.

I don’t think so. I don’t presume that modern prokaryotes are the same as ancestral prokaryotes, but even under the front-loading hypothesis common descent is presumed. That means that modern prokaryotes are descended from the ancestral prokaryotic super-cell that contained the coding for every single later development, from the flagellum to the blood clotting cascade to wings and lungs and the human brain. If the ancestral form contains all of those genes, then the descendant would have them as well, still unexpressed of course. Unless, as I said above, one posits some magical mechanism by which all of those later traits, and only those traits, would disappear from the genome. Even in organisms where a phenotypic trait has disappeared (like eyes in cave dwellers), I don’t believe the gene for that trait just disappears from the genome; it stays there and is switched off and over time becomes useless because of mutations (correct me if I’m wrong on that). And also bear in mind that if front loading and common descent are both true, then all that coding for relatively recent traits had to be present not only in prokaryotes but in every single descendant species in the chain from prokaryotes to the time when the extent species evolved with a need for that gene to be active. But then, again, one must posit the magical disappearance of that gene not only from prokaryotes but from every single species in the lineage leading to that modern organism.
#24 jba
June 8, 2007

“She had a very long and detailed explanation for why God did it that way”

Did she actually think she understood *why* god did something? Of course I have a friend who is positive she knows her gods thoughts/reasons/etc. And of course, he completely agrees with her on everything. :>
#25 Royale
June 8, 2007

In my evolution class as an undergrad, my professor stressed the importance of, for lack of a better term, cellular economics. Basically, cells must be efficient, both in mass and energy. Hence, organisms must be efficient. The least efficient cells or organisms are least likely to survive and pass on their genome.

So, extrapolating from that, I’m trying to analyze this. Let me know if I make a logical fallacy.

If I understand the front-loading hypothesis to be many un-expressed genes, it seems grossly inefficient, particularly for prokaryotes.

Now, vertebrate genome is quite inefficient, look to our satellite DNA, etc…However, that inefficiency is compensated by our overall mass – basically, we can afford to be (again, cellular economics).

But a prokaryote is just one cell. So, to pack in a whole of genes which are essentially dead weight only creates a selection pressure against that organism as compared to another prokaryote that has lost the unexpressed genes.

As such, over time, those organisms would be excluded from the gene pool.

Now, all this presumes a selection pressure based on these unexpressed genes. If others know more, please chime in.
#26 DuWayne
June 8, 2007

jba -

I think it was more of a suspicion as to why God would do it that way, not an absolute. What I find rather frightening about her reasoning, is that she was raised by atheist parents and by all accounts was a rather harsh atheist in high school (I didn’t know her back then, but she was then the girlfriend of one of my closest friends). She fully accepted and understood evolution and evolutionary mechanisms. Her husband, also a very close friend of mine and how I became friends with her, has a masters in chemical engineering.

She came to accept OEC/ID after reading a fairly popular book, among OECs, that I can’t recall the title or author of, off the top of my head. Her husband is not so sure about it, but has come to accept that macroevolution may well be false. He and I have had some rather interesting discussions about it, as he got a far stronger background in biological evolution in school, than I ever did. Her educational background ended up in law, but she too has a decent grounding in science, having originally majored in zoology. Both of them have, to different degrees, rejected the science education they received, as it seems to them to conflict with their faith. The wife going as far as telling me that she prays that I will come to understand the outright lies of evolution, so as to truly accept our faith. Scary stuff.
#27 sinned34
June 8, 2007

Well, duh. This is all very simple, people! God preserved all the front-loaded information from the Original Cell. The genome didn’t start to collect errors until after The Fall when Adam sinned! That’s why all cells these days don’t show all the front-loaded information: they aren’t Perfect anymore!

Silly evolutionists!
#28 Louis
June 8, 2007

So Begley and evolutionists have so much faith in the story of evolution, that they are going to force the world to buy into a 400 billion year old story that no human was able to document?!?!?!

Scientists were never here in the beginning of time, neither anyone else for that matter. Evolution is just another idea without any scientific merit. It can not be replicated and can not be used to predict our next evolutionary phase. A scientist cannot recreate the evolutionary process in a lab, and just because an offspring takes on characteristics of both parents (micro evolution)… that does not mean they will transform into another species.

Science is about fact, and evolution appears to have none. Evolution is like a puzzle, with large pieces missing and scientists filling in those pieces with their own ideas. The fossil gaps and past data temperings by huxley etc… are just proof of how outdated this idea has become. Rational people will ask how and why, before they put their trust and belief in a pseudo-science such as evolution and ID.
#29 G Barnett
June 8, 2007

Ok, Louis, just what is the alternative, hrm? An anti-intellectual, non-rigorous and totally unsupported by any evidence whatsoever assertion of “Goddidit?”

Also, you might want to check out the definition of Pseudoscience before trying to apply it to Evolution (though I’ll agree wholeheartedly that it certainly applies to ID).

I’ll let everyone else play “spot the canard” with your post — it certainly is a target-rich-environment.
#30 386sx
June 8, 2007

Science Avenger wrote: Which is exactly what they’ll do. They’ll invent a “loaded cohesiveness” to keep the front loaded genetic information from unravelling, just like they invented the “genetic limit” to keep microevolution from becoming macroevolution.

Right. Mr. Brayton makes it sound like creationists think it’s a bad thing for creationists to invoke magical mystical thingies. Yeah, they have to invoke magic spells and miracles, boy you really got those guys in a corner now! Silly Mr. Brayton.

J-Dog wrote: Hey Linda Parsons – WOW! What a coincidence! The Lord just appeared to me in a vision last night, and he said you should bite me!

Good heavens man, what on earth are you talking about.
#31 Richard Simons
June 8, 2007

A scientist cannot recreate the evolutionary process in a lab

Anyone who can write this (quite apart from the other blunders) needs to do some serious reading before they comment on a blog about evolution.

As regards front-loading, I am puzzled as to what the point of it might be. If the first organisms were created with all the ‘information’ for all subsequent organisms squashed inside their bodies (there might be a packing problem there) why not just throw all the switches right then and there rather than spend millions of years going through all the intermediate steps?
#32 Coin
June 8, 2007

The fossil gaps and past data temperings by huxley etc… are just proof of how outdated this idea has become.

Wait. “Huxley”? You mean Thomas H. Huxley, 1825-1895?

Are you sure it’s evolution with the outdated perspective here?
#33 Ed Brayton
June 8, 2007

Louis wrote:

So Begley and evolutionists have so much faith in the story of evolution, that they are going to force the world to buy into a 400 billion year old story that no human was able to document?!?!?!

400 billion years? What on earth are you babbling about?

Scientists were never here in the beginning of time, neither anyone else for that matter. Evolution is just another idea without any scientific merit. It can not be replicated and can not be used to predict our next evolutionary phase. A scientist cannot recreate the evolutionary process in a lab, and just because an offspring takes on characteristics of both parents (micro evolution)… that does not mean they will transform into another species.

This idea that because there was no one there to observe it, it can’t be scientifically studied is just plain idiotic. We convict people and send them to death every day without anyone there to witness their crime. The reason is obvious: we do not need to observe something happening in order to study it and explain how it happened. We do this through the application of basic logic. We can’t recreate the solar system in a lab either; does that mean we can’t identify the orbits and make predictions? Of course not.
#34 sparkles
June 8, 2007

It’s tempting to ignore the Answers in Genesis folks, because they had retreated on the lobbying front. It is not a message of ecumenical dialogue. It is one of proselytizing.

Proselytizing in and of itself is fine with me. Although it isn’t for me, I can certainly appreciate the honest, sincere zeal most people engaged in missionary or proselytizing activity have for their message of salvation.

What I have a problem with is how the Answers in Genesis movement twists science — repeatedly taking facts out of context — in order to misrepresent what scientists do and say. I doubt they do it with deliberate intent to mislead, but leading creation scientists do it unambiguously and quite assiduously in newsletters, blogs and even books. And given the importance of education in general — critical thinking and handling of complex information in a changing world — creation scientists cannot have a directly positive effect on folks’ understanding of science or their skill in handling and critiquing information and messages coming from various sources of authority, whether its the science lab or the pulpit

Once again this article presented by Ed shows creationist theory ignores factual evidence of evolution to meet their needs of proselytizing activity. And in the end, what the creationist theorists are creating is a generation of people who don’t ask questions, don’t have critical thinking skills and won’t be able to solve problems. That in itself is scary.
#35 kehrsam
June 8, 2007

Louis: I can’t see you, and wasn’t there when you typed your post; neither can I replicate it in my lab: Therefore, neither it — nor you — exist. QED

Next I will prove the existence of Odin through numerological references in Beowulf. Well, the Classic Comics version, anyway.
#36 sparkles
June 8, 2007

Ed, I find the argument no one was there to observe evolution millions of years ago quite humorous. The same premise can be said about God and his creation. No one saw it, so it must not be so. See how that works?
#37 grasshopper
June 8, 2007

From EJ’s post

“…Front-loadists would say that we *might* see that some prokaryotes have a lot of genes that have never been “switched-on”, but we wouldn’t necessarily. … “

Rather than searching for a rabbit in the pre-cambrian perhaps IDists would find it easier to find a prokaryote oozing switched-off genes.
#38 Science Avenger
June 8, 2007

I nominate Louis for this month’s Gish Award for his wonderous gallop.
#39 DAVID
June 8, 2007

FOR THE ISLAMIC TAKE ON DARWIN ETC. SEE:

http://www.harunyahya.com/

Scary!
#40 DAVID
June 8, 2007

FOR THE ISLAMIC TAKE ON DARWIN ETC. SEE:

http://www.harunyahya.com/

Scary!
#41 Allen MacNeill
June 8, 2007

Louis is either a troll or monumentally undereducated. Given the time of night and the blythe nonsensicality of his post, I’m going with the former hypothesis.
#42 Captain Howdy
June 9, 2007

Big point by grasshopper–if front loading is for real, there ought to be quite a few examples of it still in nature, so they ought to have plenty of contemporary examples. Do Behe or Minnich or any of the other IDeologues give any?

That’s an actual question. I have so far been unable to bring myself to read DBB–or this new one–so I really don’t know if Behe gives examples in nature or not.

But, if he doesn’t have convincing examples, that would be damaging, I think. Lugging around some genetic library that wasn’t being expressed somehow seems a lot to ask of the lowly prokaryote.
#43 Ed Brayton
June 9, 2007

It’s even worse than that, actually. If the original prokaryote was a front-loaded supercell with the genes necessary for every single IC system that would be needed over the next 4 billion years and then spawned thousands of descendant species of prokaryotes and millions of species of eukaryotes long before any of them were needed, those genes had to disappear independently from every one of those species.
#44 Another predictable argument against front-loading
June 10, 2007

Quoted from:
Another predictable argument against front-loading
by Krauze

[...]

The bad news is that Brayton then goes on to criticize front-loading, getting the whole concept wrong and making all the same old mistakes that he should be too intelligent to fall for. The trouble starts with the very title of his post, “Exaptation vs Front Loading: Why Evolution Wins”.

[...]

Brayton often makes fun – and justifiably so – of creationists who criticize evolution without having tried to understand it. Maybe he should heed his own advice and read up on that concept he’s trying to criticize.
#45 Wiliam Bradford
June 10, 2007

Ed Brayton writes:

It’s even worse than that, actually. If the original prokaryote was a front-loaded supercell with the genes necessary for every single IC system that would be needed over the next 4 billion years and then spawned thousands of descendant species of prokaryotes and millions of species of eukaryotes long before any of them were needed, those genes had to disappear independently from every one of those species.

If the original prokaryote was front loaded with the genes necessary to enable replication, maintenance of genomic integrity and adaptive changes, that alone could suffice. The actual specific genes of future IC systems could emerge through a process made possible by genes enabling the basic functions alluded to.
#46 Thought Provoker (aka Quantum Quack)
June 10, 2007

Hi Ed,

Thank you for providing this interesting post and the link to the paper about sponge genes. I have been being a gadfly in both Telic Thoughts and Pharyngula by presenting my version of the Penrose-Hameroff model. I earned the designation “Quantum Quack” at Pharyngula. Your post generated some interest in Telic Thoughts, so I thought I would give you the opportunaty to take a swipe (swat?) at me.

Here is the conclusion of the paper you linked…

Highly conserved protein interaction motifs and co-expression in sponges of multiple proteins whose homologs interact in eumetazoan synapses indicate that a complex protein scaffold was present at the origin of animals, perhaps predating nervous systems. A relatively small number of crucial innovations to this pre-existing structure may represent the founding changes that led to a post-synaptic element.

I agree this piece of scientific evidence potentially provides an interesting insight into understanding something, but what?

Here are three possibilities…

1. An accidental feature that serendipitously shaped synaptic development in life on Earth.

2. Intelligent front-loaded feature created for the direct purpose of shaping synaptic development in life on Earth.

3. A pre-determined, retrocausual feature forced by the inevitable synaptic development in life on Earth.

Rather than put my spin on the first two hypotheses, I will further explain my version of the Penrose-Hameroff model and how this evidence supports it.

If you think about a computerized pseudo random number generator, it really isn’t random, just complex. All of the numbers are pre-determined. The assumption is that this simulates some real-world randomness. Hopefully, you can understand how Newtonian physics implies, at a macro level, matter acts in a deterministic manner, even if it is complex. It isn’t until you get down to the quantum mechanical level that things become non-deterministic. Historically, we have just assumed quantum effects are random. Penrose suggests quantum effects aren’t random, just non-deterministic and non-local. In other words, quantum effects have to be consistent with all other non-local quantum effects in our space-time universe which includes all time (past, present and future) in addition to all locations.

An effect that is driven by all other effects in the Universe for all time would be so complex that it would be almost indistinguishable from randomness. “Almost” being the operative word. Evidence of the universe appearing to “magically” force consistency would provide hints that the Penrose-Hameroff is scientifically accurate. I suggest the appearance of a “pre-existing structure…that led to a post-synaptic element” would be just the kind of evidence we should be looking for. Especially, since Penrose-Hameroff is also suggesting synaptic activity can be directly traced to quantum mechanics.

Provoking Thought
#47 Ed Brayton
June 10, 2007

William Bradford wrote:

If the original prokaryote was front loaded with the genes necessary to enable replication, maintenance of genomic integrity and adaptive changes, that alone could suffice. The actual specific genes of future IC systems could emerge through a process made possible by genes enabling the basic functions alluded to.

Translation: if God had magically put the genes in there and did something to magically protect them from the natural process of mutation and did it in such a way that it would precisely mimic evolution, we’ve solved the problem. Tell me something: how would we discern the validity of this idea from the invalidity of standard evolutionary theory?
#48 Thought Provoker (aka Quantum Quack)
June 10, 2007

Ed Brayton asked…

Tell me something: how would we discern the validity of this idea from the invalidity of standard evolutionary theory?

Thank you for responding.

We are having parallel discussions on Telic Thought link

Here was Bradford and my joint answer to that question…

“Physical evidence that appears to “magically” provide universal consistency.

Something that looks like a reverse of a cause and effect relationship (retrocausality) would be the kind of thing we might be able to detect.”

I suspect a typical ID response would also include “How many coincidences would it take to convince you there are too many?”

Personally, I am interested in your opinion of Penrose-Hameroff. I can provide lots of links explaining it if you are interested.
#49 Ed Brayton
June 10, 2007

Thought Provoker:

I wasn’t responding to you, I was responding to Bradford. It is his response that I’m interested in. I don’t have the foggiest idea what you’ve been talking about.
#50 Art
June 10, 2007

The proponents of front-loading (“FLE”), in trying to accommodate reality, have constructed a framework that is indistinguishable from what they would call “unguided evolution”. The only conceptual difference is that they posit, somewhere, somehow, some interference. Of course, by mechanisms that we are not supposed to know or even decipher by the scientific method, by an “intelligence” we’re not supposed to know or question.

There’s no need for such interference and precisely zero evidence that such events ever occurred. There is no need for FLE. Plain old “E” works just fine.
#51 Ed Brayton
June 10, 2007

Art-

Exactly right. They are positing that something (but not God, wink wink) somewhere did something to make sure that evolution unfolded the way it did in a manner that would precisely mimic evolution, making it indistinguishable from evolution. But this is supposed to be a meaningful statement?
#52 Thought Provoker (aka Quantum Quack)
June 10, 2007

To both Art and Ed -

Excuse me for coming out of left field, but I have been trying to find anything valuable in the ID arguments (ok, so I am a masochist).

While I believe most ID proponents are just looking for a scientific excuse to believe in God, there are some that make a reasonable argument or at least presents some thought provoking evidence.

For what it is worth, I think sometimes you are too ready to assume there is nothing there just because 99% of it is garbage. My old engineer professor used to warn us not to throw the baby out with the bathwater when we are analyzing problems. I have tried to heed that advice.

When you get the time, take a look at this. You may find it hard to dismiss. Note that Penrose isn’t some unknown quack. He, along with Hawking, mathematically described Black Holes. Penrose knows his quantum mechanics.

I am not suggesting this is ID. All I am suggesting is that there may be something here. I chuckle to myself every time I think of the possibility that evidence for ID made lead to a discovery that most ID proponents would abhor, a scientific explanation for front-loading and free will.

Provoking Thought
#53 Wiliam Bradford
June 10, 2007

Ed: Translation: if God had magically put the genes in there and did something to magically protect them from the natural process of mutation and did it in such a way that it would precisely mimic evolution, we’ve solved the problem. Tell me something: how would we discern the validity of this idea from the invalidity of standard evolutionary theory?

Ed, before you get evaluate evolution you need a replicating organism having a capacity to evolve. It was you who invoked an original prokaryote in your critique of FL. What evolutionary process would be mimicked in the pathway that led to this initial prokaryote? The question that logically preceeds the one you posed is how would we discern a pathway to an original prokaryote. When you have such a pathway we can proceed to comparative assessments.
#54 386sx
June 10, 2007

Ed, before you get evaluate evolution you need a replicating organism having a capacity to evolve.

Says who? Nice try though.
#55 Wiliam Bradford
June 10, 2007

“Says who? Nice try though.”

Evolution does not entail a replicating organism with a capacity to evolve? Who’s dealing with magic then?
#56 386sx
June 10, 2007

Evolution does not entail a replicating organism with a capacity to evolve?

Evolution entails a replicating organism but it doesn’t need a capacity to evolve because its big mommy up there in the sky can make it do whatever she wants it to do with magic “poof” rays.

Who’s dealing with magic then?

I dunno. Not me. (I’m being very scientifical.)
#57 Ed Brayton
June 10, 2007

I wrote:

Ed: Translation: if God had magically put the genes in there and did something to magically protect them from the natural process of mutation and did it in such a way that it would precisely mimic evolution, we’ve solved the problem. Tell me something: how would we discern the validity of this idea from the invalidity of standard evolutionary theory?

And William Bradford executed a perfect Gish Gallop with this answer:

Ed, before you get evaluate evolution you need a replicating organism having a capacity to evolve. It was you who invoked an original prokaryote in your critique of FL. What evolutionary process would be mimicked in the pathway that led to this initial prokaryote? The question that logically preceeds the one you posed is how would we discern a pathway to an original prokaryote. When you have such a pathway we can proceed to comparative assessments.

I call this a Gish Gallop because that is precisely what it is, an attempt to change the subject. The subject here is exaptation vs front-loading and the specific question I asked you to answer was how it would be possible to distinguish between those two possible explanations. You didn’t even attempt to answer that question, choosing instead to try to change the subject from evolution to abiogenesis. How that first self-replicating organism came to be is certainly a fascinating subject and one with several possible, none of which I am at all ready to declare the answer. But it is still an entirely separate question from the one under discussion.

If it will make you feel better, let us presume that the first self-replicating organism, likely some sort of proto-cell of some sort, was placed on earth by God. For the purposes of this discussion, as attorneys like to say, I will stipulate that fact. But that does not help you answer the question I posed to you. Even if we presume that the first self-replicating life form was placed here by God, that does not logically support the claim that he front-loaded the first cell with the genetic coding for every single future evolutionary development necessary for the creation of the millions and millions of species that would evolve over the next 4 billion years. My question remains: how do you propose to determine whether new complex traits evolved by selective tinkering with pre-existing traits, or were programmed in at the beginning and therefore made the evolutionary history of life on earth inevitable and predetermined? What sort of predictions would the front-loading explanation make that exaptation would not, predictions that would help us discern which one is true?

I can think of several answers, a couple of which I’ve mentioned above. One is that, if true, the genomes of the most primitive organisms (those most closely related and less diversified from the original super-cell organism) should be chock full of all of that extra genetic coding they didn’t need. Another is that if all future evolutionary developments were predetermined and pre-programmed in before the evolution of life began, it makes little sense that 99% of the species that have ever lived have gone extinct (why program in the development of millions and millions of organisms, coding to make sure they’re adapted to their environment, only to have them die out after a relatively short period of time when they are no longer well adapted?). Surely a being capable of planning out the future so meticulously as to make sure that a bacterium had the genetic coding for the development of the human brain could have done so without having 99% of his handiwork killed off. There are other predictions, all of which tend to support exaptation rather than front-loading by a designer with a grand plan, but we’ll leave it there for now.

P.S. I give you a 9.5 for the Gish Gallop. You would have scored better, but you didn’t stick the landing.
#58 Skemono
June 10, 2007

Ed, before you get evaluate evolution you need a replicating organism having a capacity to evolve.

Wouldn’t that be every biological organism on the planet? ‘Cause I’m pretty sure we’ve got plenty of those.
#59 Art
June 10, 2007

Art’s rule – anytime an ID antievolutionist (like Bradford) invokes the OOL from out of the blue, (s)he is admitting that (s)he has no answer to the criticisms or arguments being put forth. Here, the criticism is that FLE and “E” are indistinguishable, except for the fact that the “FLE”-er has a need to insert something where nothing is needed or exists.

OK, so we’ve settled that issue. Not that there was much doubt about the vacuity of FLE. But it’s nice to see the OOL invoked at this early juncture- sort of spells out clearly the poverty of the teleological position.
#60 386sx
June 10, 2007

Wouldn’t that be every biological organism on the planet? ‘Cause I’m pretty sure we’ve got plenty of those.

Even if he were satisfied with that there would still be plenty of gaps for his supernatural world to hide in. Before you can have an organism on the planet, first you need a planet. Before you can have a planet, first you need a universe. Not that there’s anything wrong with not being satisfied with an answer. But how would we ever find anything out if we invoke magic when something is difficult or when we don’t like something? It doesn’t seem very productive. Maybe if scientists would do some experiments and see how the magic rays from the sky work then we could make some progress on this issue, hardy har har.
#61 Hawks
June 10, 2007

Ed wrote:
As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed….
…
they have to posit that God not only loaded the genes for all those later developments in to earlier organisms that didn’t need them, but he also put some sort of mystical force field around them to prevent them from mutating over the last 4 billion years.

DaveScot at uncommondescent has his own answer to this: error checking a la computers. Unfortunately, given that there is no evidence what-so-ever that there actually is/was any error checking going on means that IDers might as well be appealing to mystical force fields anyway.

Front loading is the idea that God (no, I’m not going to engage in the ridiculous fiction that the generic designer they posit is anything other than God)…

It doesn’t really matter if you posit this or many other potential designers. The terms “intelligent designer” and “god” are interchangeable when discussing ID. Don’t feel that you have to explain yourself.
#62 John Marley
June 10, 2007

FOR THE ISLAMIC TAKE ON DARWIN ETC. SEE:

http://www.harunyahya.com/

Scary!

Well, at least the site was pretty.
#63 Wiliam Bradford
June 11, 2007

Ed: If it will make you feel better, let us presume that the first self-replicating organism, likely some sort of proto-cell of some sort, was placed on earth by God. For the purposes of this discussion, as attorneys like to say, I will stipulate that fact. But that does not help you answer the question I posed to you. Even if we presume that the first self-replicating life form was placed here by God, that does not logically support the claim that he front-loaded the first cell with the genetic coding for every single future evolutionary development necessary for the creation of the millions and millions of species that would evolve over the next 4 billion years.

If evolution requires a self-replicating life form replete with a genetic code and a genome and you have that, then you also have a capacity for mutations and a selection process. If you have the raw materials for an evolutionary process then the essential elements of the process were front loaded. Evolution would have had to have been front loaded at point of origins. You wrote:

“Front loading is the idea that God (no, I’m not going to engage in the ridiculous fiction that the generic designer they posit is anything other than God) programmed in all of the genetic information necessary for later developments in to the first cell.”

Given your stipulation either all the genetic information making possible subsequent change was present or there is something amiss with standard theory. You have a genome, a means of change and selection. Of course, all the genes and functions found among biological organisms were not present. But who told you that was a prerequisite to front loading?
#64 Ed Brayton
June 11, 2007

And once again, you evade the question. You write:

If evolution requires a self-replicating life form replete with a genetic code and a genome and you have that, then you also have a capacity for mutations and a selection process. If you have the raw materials for an evolutionary process then the essential elements of the process were front loaded. Evolution would have had to have been front loaded at point of origins.

This is gibberish. You have done nothing but redefine front-loading as “the existence of a self-replicating organism.” The existence of a self-replicating organism, however it got there, is not synonymous with front-loading. If it was, all those arguments we hear about the alleged impossibility of a new complex trait developing in an organism that didn’t have that trait previously are rendered completely irrelevant. This is yet another example of the Gish Gallop – the definition of “front-loading” appears to be whatever you want it to be at any given time.

You have a genome, a means of change and selection. Of course, all the genes and functions found among biological organisms were not present. But who told you that was a prerequisite to front loading?

If having an orgamism capable of change and selection is all that is needed to conclude “front-loading”, then there is no distinction between evolution and front-loading. Again, all those anti-evolutionary arguments become completely pointless. Which means there’s a reason why you’re not answering my question – you can’t. Because you are defining front loading as being identical to evolution. This is not even approaching a coherent idea.
#65 William Bradford
June 11, 2007

If having an orgamism capable of change and selection is all that is needed to conclude “front-loading”, then there is no distinction between evolution and front-loading.

Of course there is. You alluded to the distinction in making one between evolution and abiogenesis. Your misconception that FL is an evolutionary process, rather than evidence that the course of evolution was influenced by initial conditions, is the source of confusion.

Again, all those anti-evolutionary arguments become completely pointless. Which means there’s a reason why you’re not answering my question – you can’t. Because you are defining front loading as being identical to evolution. This is not even approaching a coherent idea.

No. Front loading seeks to explain evolution by reference to initial parameters. The initial basics previously mentioned- the genetic code and essential cellular functions enabling replication- if varied, could have led to different outcomes. The ID vs. evolution meme has always been a strawman. It seeks to artificially confine the discussion of natural history.
#66 Sean
June 11, 2007

Of course, all the genes and functions found among biological organisms were not present. But who told you that was a prerequisite to front loading?

So partial front loading?

Eyeballs, microscopic butt propellers and stink bug rear ends were front loaded? Panda thumbs evolved?

What is the technique to decide which features were in the original release and which cropped up later?
#67 Art
June 11, 2007

Of course, I anticipated the concept of FLE almost 6 years ago.

Front loaders don’t have a positive case to make for placing the intervention at the OOL, or at any other time. This is just the convenient “we don’t kow, thus design” placeholder du jour.

Design advocates have never really wrapped their minds around the Universal Rule of Design, for what it’s worth.
#68 Jeff Hebert
June 11, 2007

William Bradford wrote:

FL is an evolutionary process, rather than evidence that the course of evolution was influenced by initial conditions, is the source of confusion.

This is as close as you’ve come so far to actually providing a definition of what you mean by FL. I even followed the links to Telic Thoughts, and in that thread too you refuse to provide a clear definition, instead pointing to other long-winded threads with lots of comments for the reader to puzzle through.

Are you incapable of providing a definition of what YOU mean by the term Front Loading, or are you unwilling to for some reason? You keep saying what FL is NOT, but you have yet to say what it IS, in your understanding of the term. It’s fairly pointless to engage in a discussion with you for that reason. No one seems to be able to guess what you mean by what you say, which they shouldn’t have to try to do in the first place — you should simply define your terms.
#69 Ed Hensley
June 11, 2007

I really enjoy your website. Keep up the good work.
#70 Ed Brayton
June 11, 2007

Jeff Hebert asks an excellent question, which I suspect Bradford will dodge as he has dodged mine. The definition of front-loading that I responded to was the one offered by Behe (and since Behe is the most prominent ID advocate in the nation, it is far more relevant than Bradford’s). But Bradford now seems to be defining front-loading all the way down to the notion that the future path of evolution was constrained by the initial conditions. That’s a “duh” statement if I’ve ever heard one. Who in their right mind would dispute it? Of course the future pathway of evolution was constrained by the initial conditions; every future event is constrained by initial conditions, as far as we can tell. He also seems to be defining front loading as “having the ability to evolve”, which of course makes it synonymous with evolution and makes any attempt to distinguish between the two meaningless.

All of that is far different than what Behe has proposed and since it is Behe who is in a position to influence public policy and not Bradford, it is his ideas we must deal with. As for the statement that “the ID vs evolution meme was always a strawman”, perhaps he would like to inform the Discovery Institute of that so they can stop making anti-evolutionary arguments all the time. This is all quite odd. The only ones who really matter in the ID movement – the only ones trying to get it shoved into public school science classrooms by any means necessary – are the folks associated with the Discovery Institute. It is their ideas we criticize. Bradford’s ideas appear to be less stupid but also far less coherent.
#71 raven
June 11, 2007

How does anyone know that god didn’t invent exaptation, LOL? There is an easy way out for OEC. Any mechanism that scientists find or theorize, god actually invented. Of course at some point their theory converges on the scientific theory. But at least they don’t look like reality denying idiots.

Front loading won’t work. The human genome is full of pseudogenes, extra genes that weren’t needed from past duplication events. They all accumulate mutations and are the molecular equivalent of fossils. Eight percent of the genome is defective retroviruses that are beat up to one extent or another. Wreckage from past invasions and battles that we can trace back far into the primate lineage. Genes that aren’t used end up like the cave fishes eyes.
#72 Dave S.
June 11, 2007

Ed writes:

That’s a “duh” statement if I’ve ever heard one. Who in their right mind would dispute it? Of course the future pathway of evolution was constrained by the initial conditions; every future event is constrained by initial conditions, as far as we can tell.

Of course you are correct. Evolution is also constrained by the formation of the Earth which happened before life came about (however initial life came about), and in turn it depends on the formation of atoms, and ultimately, of the universe itself. … Which of course itself depends on conditions that prevailed before (if ‘before’ has any meaning in this context) the Big Bang.

This is merely an attempt to push ID, by using some vague undefined notion of ‘front loading’, to a realm where it cannot be tested. Not that the traditional ID notions can thermselves be tested! True, it can’t then be rejected scientifically, but that is only accomplished by making it sterile scientifically. Much inferior to “we don’t know”. It’s like a child who keeps asking ‘but what came before THAT?’ ad nauseam.

ID advocates are famous for refusing to discuss intelligent design, because there is nothing to discuss. So instead they attack evolution as a surrogate for supporting ID, and hope nobody will notice.
#73 raven
June 11, 2007

Louis:

A scientist cannot recreate the evolutionary process in a lab, and just because an offspring takes on characteristics of both parents (micro evolution)… that does not mean they will transform into another species.

This guy is just reading off the old, tired creo deck of 3X5 cards. It was wrong at the start and repeating decades old lies doesn’t make them true.

Actually evolution is quite accessible to experimental verification and a lot of work has been done in both the lab and field. Not only does it work but medically and agriculturally is very important. The problem comes with trying to test some of the larger pieces. To evolve from one species to another takes a large population, some selection pressure, and a few tens of thousands to a few millions of years. Try getting grant funding for a ten thousand year experiment.

There have been some natural experiments in progress that we can watch as a slice in time. Adaptive radiation in Galapogos finches, Hawaiian drosophila, African cichlid fishes and so on. And in near historic times we have seen wolves transition to dogs, teosinte to corn, and a chimp virus into a vicious human pathogen, HIV. Macroevolution is just microevolution repeated stepwise.
#74 Salim Fadhley
June 11, 2007

To evolve from one species to another takes a large population, some selection pressure, and a few tens of thousands to a few millions of years. Try getting grant funding for a ten thousand year experiment.

Not so!

Under the right conditions, speciation can occur very quickly. It’s adaptation that takes a long time.

http://evolutionlist.blogspot.com/2006/11/island-mice-may-evolve-faster-from-one.html

In this case, a small population, benign environment and physical separation from other breeding groups are the magic formula.
#75 Cowardly Dismebodied Voice
June 11, 2007

If front loading were true, it would mean that we would know exactly what next year’s killer flu virus was going to be – we only need to dissect the genome of this year’s version, and see what genes aren’t working.

Seems like a worthwhile research project. It really can’t be that difficult, viral genomes aren’t all that large.

However I am not holding my breath waiting for a breakthrough. These people make up crap on the fly to explain how their theories never lead to worthwhile methods of helping people.

Or, the ancestor of the 2008 virus is hiding under a rock right now, with all its front loaded genes intact, waiting for new years’s day.
#76 Dave S.
June 11, 2007

Macroevolution is just microevolution repeated stepwise.

1. Maybe. Some changes, especially early on in the history of life, may have involved mechanisms other than those identified for microevolutionary changes. I don’t think the jury is in on that one yet.

2. One should be clear that the argument for macroevolution is not macroevolution = microevolution + time, as some of the more troglyditic creationists might think. The independent evidence for macroevolution, and there’s plenty of it, exists today. There is simply no other testable biological explanation.

It’s the observations of the evidence that is reproduced, not the events as Louis may think.
#77 analyysi
June 11, 2007

Ed Brayton wrote:
The definition of front-loading that I responded to was the one offered by Behe (and since Behe is the most prominent ID advocate in the nation, it is far more relevant than Bradford’s).

You claimed that “the definition of front-loading” that you responded to was the one offered by Behe. But has Behe really defined the term “front-loading?” I have never heard that Behe had even used the term “front-loading”. (Mike Gene has.)

Ed Brayton, could you give us a source, where Behe is using the term “front-loading”?
#78 analyysi
June 11, 2007

I meant that Mike Gene has used the term “front-loading”.
#79 raven
June 11, 2007

Not so!
Under the right conditions, speciation can occur very quickly. It’s adaptation that takes a long time.

http://evolutionlist.blogspot.com/2006/11/island-mice-may-evolve-faster-from-one.html

In this case, a small population, benign environment and physical separation from other breeding groups are the magic formula.
Posted by: Salim Fadhley

From the link:
Island Mice May Evolve Faster: From One Species To Six In 500 Years

SOURCE: Genome News Network
AUTHOR: Bijal P. Trivedi
COMMENTARY: Allen MacNeill

An alert Evolution List reader has already pointed me to an article that first appeared on April 28, 2000, concerning the unusually rapid speciation of common European mice on the island of Madeira. Apparently, these mice were brought to the island on sailing ships, most likely from Portugal. Since such ships were very small, the total size of the founding populations would have been extremely small; probably less than a dozen individuals (and certainly less than a hundred).

This would certainly qualify as precisely the kind of founder population that I described in the previous post concerning a possible mechanism for chromosomal speciation. In particular, it is extremely interesting that the mice in question have apparently speciated in less than 500 years, and that the mechanism underlying this speciation has involved multiple chromosomal fusions.

Here’s the full article describing the research (commentary follows):

Interesting paper. This would be an extreme case, as they note. It would also qualify as a “natural” experiment. It also shows why biologists have difficulty designing experiments to demonstrate speciation. Who is going to start an experiment and let it run for 500 years? Maybe if Louis put down his creo deck of 3X5 cards and read some real research, he would learn something.
#80 Bill Gascoyne
June 11, 2007

Actually, Star Trek beat Behe to the “front-loading” punch by three years. (See Star Trek TNG episode 146, “The Chase” from Season 6).
#81 harold
June 11, 2007

Both the term “front loading” and the term “intelligent design” were up front designed to provoke confusion, and we see time and time again that it works.

Regardless of whether Behe himself ever uses the term “front loading”, or whether it is used mainly by other creationists, William Bradford apparently thinks it simply means that the first replicating life was created by God in a way that confined subsequent evolution, so that humans could evolve, if I understand him correctly.

That may or may not be a sophisticated “god of the gaps” argument – it sounds like one to me, and I don’t agree with it, even though I’m not an atheist per se – but it’s an argument that is not at odds with modern science for the time being.

That is NOT what creationists mean by “front loading”, what they mean is that no sequence of genetic material can ever mutate to code for a new functional protein or nucleic acid, so some crazy protocell had to be jammed with every gene that would ever come to exist.

Many quite intelligent people I meet think that they accept “intelligent design” because they think, from the words, that it’s a benign “theistic evolution” type of idea. It isn’t. It was designed to pander politically to YEC authoritarians, and it is grounded in illogical arguments that deny well-established scientific fact.

The point of the DI and ID is to deny mainstream scientific understanding of evolution. That’s what they themselves say, over and over again. Philosophical ideas about God that can be true, even in the context of the observed evolution of life on earth, are not of interest to them.

If your personal belief is that science describes the universe, but God did something magic at the beginning of time to make it turn out this way, or something along those lines, I personally have no beef with that non-testable philosophical idea, but don’t call it “intelligent design”, that’s taken.

Also, if you’re a YEC creationist, admit that rather than going on about “intelligent design”. Please.
#82 Ed Brayton
June 11, 2007

analyysi-

What difference does it make whether Behe actually used that term? What he describes clearly IS front-loading. Whether he calls it that or not, it is that idea that I was responding to.
#83 Gerard Harbison
June 11, 2007

It isn’t until you get down to the quantum mechanical level that things become non-deterministic

I suppose calling oneself ‘quantum quack’ is fair warning. Still, please take any formulation of the Schrödinger equation, time-dependent or -independent, non-relativistic or relativisitic, and identify for me what term allows for indeterminacy in evolution of the wavefunction.

Oh, and when you’ve figured that out, tell Penrose.
#84 Thought Provoker (aka Quantum Quack)
June 11, 2007

Hi Gerard,

You wrote…

Oh, and when you’ve figured that out, tell Penrose.

Are you kidding?!?!? To a Quantum Quack like me, Penrose represents the second coming. I wouldn’t dare. ;->

Thanks for feeding the troll… err.. um… quack.
#85 Unsympathetic reader
June 11, 2007

How deterministic and useful is front-loading in evolution, ID-style? Based on Behe’s recent claims about the need for frequent tweaking over the course of evolution, I’d conclude that he thinks the “unfolding” of front-loaded systems is extremely limited at bringing about evolutionary change. Is it valid to even call anything ‘front-loaded’ if it cannot support evolution without perpetual, interruptive intervention?
#86 PvM
June 12, 2007

And yet Mike Gene still ‘argues’

Does Front Loading necessarily imply a designer. Yes or no?

Yes, I’d say that front-loading entails foresight coupled with an objective, which speaks to a mind.

So we have front loading being indistinguishable from regular evolutionary processes and in addition it requires a ‘mind’ and still IDists seem to think that there is anything to their thesis, especially without addressing anything more about this ‘mind’. Mike objects to people asking about the designer as being irrelevant and yet in order to compete ID will have to address these uncomfortable issues of ‘a mind’ (wink wink).

The front loading hypothesis is the weakest form of ID and while looking backwards in time, we may be amazed how life got here, to confuse this with design is just inexcusable without more evidential support.

What vacuous nonsense.
#87 386sx
June 12, 2007

So we have front loading being indistinguishable from regular evolutionary processes and in addition it requires a ‘mind’ and still IDists seem to think that there is anything to their thesis, especially without addressing anything more about this ‘mind’.

If there was a mind behind all of that then why wouldn’t they be curious about what that mind was and how it did what it did? Why just be satisfied with knowing that the mind “just dunnit”?

And in related vacuous nonsense news: If there is a god who performs miracles or communicates with people then why is there no curiosity about how this god does the miracles thingy or about how it communicates with people. What is the process behind all of that? Why just be satisfied with knowing that the god “just dunnit”?
#88 Salim Fadhley
June 12, 2007

If there was a mind behind all of that then why wouldn’t they be curious about what that mind was and how it did what it did? Why just be satisfied with knowing that the mind “just dunnit”?

Don’t look behind the curtain!
#89 Ron Okimoto
June 12, 2007

QUOTE:
Quite right. But remember, some of those genes are highly conserved or 100% conserved – that is, identical or nearly identical – between sponges and humans. And while front loading means those genes had to be “turned off” for hundreds of millions of years, exaptation posits that those genes were turned on, expressed in the phenotype and serving different functions. Thus, exaptation is consistent with the preservation of those genes while front loading is not.
END QUOTE:

I think that you are overstating the “100%” conservation. The article only claims that the residues responsible certain functions are 100% conserved. There are something like 5 “invariant” residues in hemoglobin, but all the other amino acid positions vary. There are some proteins that are pretty much invariant like histones that might only have a single amino acid difference between plants and animals, but they aren’t common and you’d have to find proteins where the entire structure was involved in its function. Not only that, but histone gene family that everyone has are likely related, but they aren’t all the same sequence, so when they do have a slightly different function they do change.
#90 One Brow
June 12, 2007

This sounds very much like the typical “limited miracle” argument. Back when I was a theist, my response would have been than an infinitely knowledgeable and powerful God would not have packed the genome with functional genes that would require mutation, but with non-functional genes that would become functional at the approriate time after all the mutations that infinite knowledge would know about ahead of time. In other words, the pre-loading would account for the mutations.
#91 Unsympathetic reader
June 12, 2007

Yeah, but there are no constraints to G*d hypotheses. One can’t argue what an undefined, unspecified designer of unknown capabilities *could* do. If, as Behe suggests, additional and frequent manipulations are required for continued evolution then pre-loading is simply not a sufficient mechanism. OTOH, if other ID advocates think that pre-loading + natural mechanisms can account for evolutionary change then they clearly are not with Behe on this but they do face the problem of distinguishibility from natural evolutionary mechanisms. Case in point: Denton is the ultimate front loader. His proposal invokes natural mechanisms after the creation of the universe.

Front-loading’s evolutionary flexibility should be a wedge issue between IDers. There are clearly some mutually incompatible opinions held in that camp. So where’s the internal debate on that?
#92 fnxtr
June 12, 2007

It’s sad, really, that their faith is so weak that they’re constantly looking for proof of God.
#93 Smokey
June 12, 2007

Ron Okimoto wrote:
“I think that you [Ed] are overstating the “100%” conservation. The article only claims that the residues responsible certain functions are 100% conserved.”

Ron is correct. The genes are homologous, not orthologous. The authors also show the domain structure of the homologs, and they are pretty far away.

I’d give you 10:1 odds that none of them are orthologous in the sense that the sponge gene would rescue a mouse null mutant.
#94 Jedidiah Palosaari
June 12, 2007

What are you talking about? The genes only had to not mutate for some 6,000 years!
#95 386sx
June 12, 2007

Don’t look behind the curtain!

Bingo dude. They fear that if they try to examine it, there ain’t going to be nothing there. They lack faith. Except for the ID people. They ain’t afraid to look because they have… faith. That’s right people. All you guys who say IDers are showing a lack of faith got it all bass backwards.
#96 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi PvM,

You noted that I had asked MikeGene on Telic Thoughts…
“Does Front Loading necessarily imply a designer. Yes or no?”
…and MikeGene responded with…
“Yes, I’d say that front-loading entails foresight coupled with an objective, which speaks to a mind.”

Which, of course, prompted you to immediately attack him about his belief in a “‘a mind’ (wink wink).”

I happen to be an Atheist but I don’t particularly care if MikeGene believes in God or not, why do you?

MikeGene may be motivated for the “wrong” reasons, but that doesn’t automatically mean his investigations are “vacuous nonsense”.

Christopher Columbus was wrong-headedly searching for an easier trade route to India. Would you call Columbus’ investigations “vacuous nonsense”?

Unless I miss my guess, science journalist Sharon Begley knew the significance of the Sponge Gene report and purposely sought to preemptively downplay its significance by setting up an ID strawman argument. Which ID proponent even mentioned the report, much less argued its significance? It looks like Sharon Begley offered a counter-argument to a strawman of her own making.

I believe there is a possibility that the Penrose-Hameroff model is true and will severely shake up both sides of the Culture War. Ed may not have the “foggiest idea” what I am talking about, but I suspect he soon will.

How many coincidences will you try to ignore before you suspect that something is there?

Even wrong-headed explorers can make profound discoveries.

Provoking Thought
#97 John
June 12, 2007

TP wrote:
“MikeGene may be motivated for the “wrong” reasons, but that doesn’t automatically mean his investigations are “vacuous nonsense”.”

Mike Gene isn’t doing anything that could credibly be described as an “investigation.” He is afraid to make predictions, so he only engages in spin after the data become available. He’s also afraid to advance a falsifiable hypothesis. Can’t you recognize his weaseling for what it is?

“Christopher Columbus was wrong-headedly searching for an easier trade route to India. Would you call Columbus’ investigations “vacuous nonsense”?”

No, I’d call your analogy vacuous nonsense, because Columbus, unlike Mike Gene, tested his hypothesis. Mike Gene has zero confidence in his.
#98 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi John,

Unfortunately for MikeGene, I can’t argue with you too strongly. Although, he has a new book coming out that I have yet to read, The Design Matrix.

While it is an easy feat, MikeGene and Telic Thoughts are among the more reasonable ID proponents. For example, they tolerate me and my “falsifiable hypothesis” (a modified Penrose-Hameroff model). It makes for some interesting conversations. It also provokes thinking, IMO.

It may also provoke MikeGene into taking more risks in presenting a model of his own. Don’t get too complacent that your default Darwinian model is the only game in town. That may not last forever, and probably won’t.

Provoking Thought
#99 John
June 12, 2007

TP,

1) What sort of seeker of truth writes a book, but refuses to make a prediction or state his hypothesis in a direct way, while writing volumes on his blog about other people? His claim that front-loaded genes can have functions makes hash of the term front-loading.

2) They may be among the more reasonable ID proponents, but they are still intellectually cowardly and dishonest.

3) Mike Gene is too cowardly to take any such risks. BTW, my models go beyond Darwin and are based on the data, not holding back and spinning the work of others, so the term “Darwinist” is ridiculous. You’ve been hanging out with ID sophists for so long that you’ve adopted their dishonest labels.

P.S. Do you see the projection dripping from the ironic title, “Another predictable argument against front-loading”?
#100 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi John,

I said “Darwinian”, not “Darwinist”.

And, yes, I noticed the irony in Krauze’s title.

I think all to often Krauze’s emotions override his better judgment.

I also suspect you guys enjoy taunting ID proponents like Krauze way too much.

Some people might begin to think you guys are arrogantly sadistic.

Provoking
#101 John
June 12, 2007

“I said “Darwinian”, not “Darwinist”.”

You did. It’s still a misrepresentation for rhetorical effect.

“I also suspect you guys enjoy taunting ID proponents like Krauze way too much.”

I enjoy taunting anti-evolution zealots. They don’t do much of anything in the positive direction other than spin.
#102 harold
June 12, 2007

Thought Provoker –

I’m confused by your posts.

I have a decent grasp of the theory of biological evolution, which some may refer to, although I usually don’t, as “Darwinian evolution”, or “Darwinism”. The way I would summarize the key points, with the necessity of oversimplication is as follows (and since what follows does not reference the supernatural, I feel tiresomely obliged to point out that I don’t consider myself an atheist, a meaningless point in this context, but one which may allow some readers to stop obsessing long enough to read what I write) –

Cellular life on earth (and post-cellular life like viruses) replicates, and replication is “imperfect”, so there is always some genetic difference between offspring and parent – that is true of either mitotic or meiotic, sexual reproduction, and it is true of cell divisions within multicellular organisms.

These variations in replicating genetic nucleic acid sequence are fully compatible with and understandable through reference to physics, chemistry, etc. There is nothing magic.

Some but not all of this variation in genetic nucleic acid sequence leads to expressed phenotypic variation.

This alone would lead to evolution (change in the frequency of alleles over time). But there is more.

Some but not all expressed phenotypic variation may impact on an organim’s interaction with its environment, in such a way that the organism’s reproductive “success” (for lack of a better word) may be impacted. For obvious reasons, variations that lead to a relatively higher rate of successful reproduction, within the very specific organismal and environmental context in which they occur, will tend to increase within a population of organisms, at least until the specific context changes in a way that reverses or neutralizes the “advantage”. This aspect of evolution is known as “natural selection”.

These well-established processes have a robust capacity to explain the physical diversity of life on earth.

You will note that none of this has anything to do with God, morality, ethics, whether life has meaning, or any other such issues. Neither, at this time, does the theory of evolution comment strongly on how life on earth originated.

My confusion is on the following point – precisely, exactly, specifically, (not arm-wavingly bullshittingly, if I may be excused for saying so), but rather, precisely and specifically, which part of the above do you disagree with, or what would you add to it to make it better?
#103 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi Harold,

I would add to it.

The impact of Penrose’s model of Quantum Mechanics is that there is no such thing as “natural” randomness. Quantum effects are non-algorithmic, non-deterministic and non-local. But NOT random.

By “non-local”, it means quantum effects are realized instantaneously everywhere in the universe, not just in a localized area bounded by the speed of light. All quantum effects are interconnected in space-time. That is everywhere in the universe and everywhen in the universe.

The past is connected to the future at the quantum level.

DNA and microtubules are small enough to directly experience quantum effects.

The future resonating with the past would express itself as retrocausality. That is a reversal of cause and effect.

The Sea Sponge gene could be an example of that.

Now you know how I earned my “Quantum Quack” designation.

Provoking Thought
#104 Ed Brayton
June 12, 2007

The past is connected to the future at the quantum level.

DNA and microtubules are small enough to directly experience quantum effects.

The future resonating with the past would express itself as retrocausality. That is a reversal of cause and effect.

The Sea Sponge gene could be an example of that.

That looks a lot like meaningless gibberish to me.
#105 John
June 12, 2007

TP,

What do microtubules have to do with any of this? There are no microtubules in either the presynaptic or postsynaptic specializations of neurons. They are actin-rich.

You’re just spewing buzzwords now.
#106 Coin
June 12, 2007

The past is connected to the future at the quantum level… The future resonating with the past would express itself as retrocausality. That is a reversal of cause and effect.

I’m beginning to see why Pharyngula gave you your nickname.
#107 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi John,

I may be confused, but I found this which includes…

Transsynaptic Signaling and Presynaptic Differentiation(A) Secreted WNT7a induces axon and growth cone remodeling during the initial stages of synapse formation. This remodeling may be achieved through regulation of the microtubule cytoskeleton…This transsynaptic junction is linked both pre- and postsynaptically to a large network of synaptic proteins via modular adaptor protein complexes…Remarkable parallels between synapse formation and growth cone motility have been observed in studies examining microtubule dynamics. Microtubule dynamic instability is considered necessary for growth cone motility, during which the microtubules attain a splayed conformation…

How does being “actin-rich” translate into “no microtubules”?
#108 fnxtr
June 12, 2007

TP(QQ) sez:

DNA and microtubules are small enough to directly experience quantum effects.

I’d be interested in seeing the empirical data backing this up. What lab tests have been done to verify this? Also whether said quantum effects are large enough to overcome/influence the usual chemical/physical behaviour of said structures.

“The past is connected to the future at the quantum level.” So what? The past and the future are connected in the quotidian sense, too. Let go of a hammer now, it’ll hit your toe in a second.

And what does “The future resonating with the past” mean? Sounds like you’ve been watching too much Star Trek. Or “What the Bleep Do We Know.”

Put down your copy of The Dancing Wu-Li Masters for a second.

Are you seriously suggesting quantum effects have transported post-synaptic protein homologues into the genomes of sponges in the distant past?

How would you prove/disprove that?
#109 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi Ed,

You wrote…
That looks a lot like meaningless gibberish to me.

Then let me try again slower.

Penrose, as in the Hawking-Penrose predictions of Black Holes. Knows his quantum mechanics and his math.

Things are very weird at the quantum level. “Heisenberg uncertainty”, “God doesn’t play dice”, “Matter is both a wave and a particle”, etc.

Penrose has developed a model that explains how quantum effects transition to, and interact with, the macro world. It involves something called “waveform collapse”. This is where all the possible quantum states collapse into one.

The interesting thing about this waveform collapse is that happens in a way that all the various observers/detectors at different locations all see the same thing. Universal consistency is forced. And it happens instantaneously (faster than the speed of light). The term “non-locality” is used.

Penrose explains that this waveform collapse is non-deterministic and non-algorithmic but NOT random.

Are you with me so far? Quite a few quantum physicists accept Penrose’s model as the best answer we have. This is not surprising considering the alternative is to assume multiple universes are constantly being created for all possible quantum states. There is also the ignore-it-and-hope-it-goes-away option crowd.

Experiments are being performed to verify Penrose’s calculations for waveform collapse. The results continue to be consistent with Penrose’s model. The model is well on its way to becoming an established scientific theory.

Even so, quite a few people still want to treat Penrose’s ideas as metaphysical and not reality and especially not macro-world reality. But it does manifest itself as macro-world reality everyday in things like the laser diodes in portable CD players.

So what are the implications of the reality of Penrose’s model?

Note that time is just another dimension in the space-time continuum. Quantum effects must not only be consistent with everywhere in the universe, it must also be consistent with everywhen in the universe. Past, present and future all play into a Penrose’s waveform collapse. This makes the outcome of a waveform collapse very complicated and very non-deterministic. For all practical purposes, it would appear to be random, but it is not.

Quantum effects also have to be consistent with all other quantum effects. The universe is totally interconnected at the quantum level for all time past, present and future events. Think of a giant Mandelbrot Set. The universe is predetermined and totally wired for consistency. We only think it’s moving because of our perception of time.

Can this quantum effect translate into biological effects?

Of course it does. It is only a matter of whether or not we can detect it. Dr. Penrose partnered up with a Dr. Hameroff to propose a Penrose-Hameroff hypothesis that tubular dimers are small enough to experience quantum level effects. These dimers make up the microtubules that are very prevalent in living organisms and may help explain why things that have no nervous systems appear to be aware of their surroundings.

Hameroff suggests that the Cambrian Explosion was a direct result of life on Earth becoming “aware”. link

I am taking it further than that but I will stop here because I suspect that you may already have an objection or three.

Provoking Thought
#110 Ed Brayton
June 12, 2007

That sounded like a lot more gibberish.
#111 Thought Provoker (aka Quantum Quack)
June 12, 2007

Hi fnxtr,

You indicated…

I’d be interested in seeing the empirical data backing this up.

One of the problems with testing for a non-deterministic effect is that it is non-deterministic. I am finding several experiments that are testing the Penrose model and Penrose-Hameroff models. I have included one. If there is interest, I can try to provide more.

Here is a link to an experiment attempting to confirm the non-locality aspect of quantum mechanics using cultured neural networks…

In recent times the interest for quantum models of brain activity has rapidly grown. The Penrose-Hameroff model assumes that microtubules inside neurons are responsible for quantum computation inside brain. Several experiments seem to indicate that EPR-like correlations are possible at the biological level. In the past year , a very intensive experimental work about this subject has been done at DiBit Labs in Milan, Italy by our research group. Our experimental set-up is made by two separated and completely shielded basins where two parts of a common human DNA neuronal culture are monitored by EEG. Our main experimental result is that, under stimulation of one culture by means of a 630 nm laser beam at 300 ms, the cross-correlation between the two cultures grows up at maximum levels. Despite at this level of understanding it is impossible to tell if the origin of this non-locality is a genuine quantum effect, our experimental data seem to strongly suggest that biological systems present non-local properties not explainable by classical models.

EPR = “Einstein-Podolsky-Rosen” which is an aspect of “quantum weirdness”. Einstein et al, argued it as a paradox, Bohm, Bell, Penrose, embraced it as reality.

Provoking Thought
#112 Coin
June 12, 2007

Penrose-Hameroff

I get the feeling that there’s a large flamewar going on somewhere else, and only one tiny corner of it has just intruded into this blog thread, so I’m afraid I’m about to step into something much bigger than I want to get into. But:

You keep invoking Penrose’s name here, and trying to drag in the Penrose Interpretation of quantum mechanics as if it were in some way linked to Penrose’s separate writings on the nature of consciousness. (As far as I know, they’re two separate ideas that just happen to have come from the same person.)

However except when you’re just reciting encyclopedia facts about some aspect of quantum theory (the Penrose Interpretation, for example) it appears that absolutely everything you’ve posted here is just copy&paste/paraphrased from one of Stuart Hameroff’s websites. Quantumconsciousness.org and all that.

Now, the thing that is interesting to me here is to compare the clear nonsense you’re spouting, to the oblique possibly-nonsense stuff on Hameroff’s websites, to the quotes I can find where Penrose talks about his ideas on consciousness. And it’s interesting because there seems to be a sharp difference in scope between each of these three things. Penrose, as far as this goes– there’s strikingly little I can find specifically and clearly said or written by him about this– seems to be primarily interested in the question of, is it possible that biological systems could experience quantum effects, and if so how can we test this? Hameroff by contrast has written a great deal, and what he has written does not seem to be beset by the same level of doubt. And more interestingly, the Hameroff stuff seems to be absolutely stuffed, just littered, with name-dropping the string “Roger Penrose”. The descriptions for his webpages put Penrose’s name, even though it appears from what I can see that everything on those pages is written by Hameroff.

So I have to wonder. What exactly is the nature of the relationship between Hameroff and Penrose? It does appear Hameroff and Penrose wrote papers together, though I don’t know how that collaboration is balanced. But it appears that many of the critical ideas being used when both of their names show up in conjunction were originally Hameroff’s. Looking at wikipedia’s entry on Hameroff, for example, I get the idea that the central thing described by “Hameroff-Penrose Hypothesis” was, in fact, an idea Hameroff had before his collaboration with Penrose began, and which Hameroff then approached Penrose about because Penrose had expressed public interest in the question of whether biological systems can leverage quantum effects.

Now, Penrose clearly does have some ideas of his own about quantum physics and consciousness which are themselves rather fringy. But at first blush what it generally looks like to me is that Hameroff and Hameroff’s followers, like the provocateur here, are mostly just using Penrose, and more specifically using his name; using Penrose’s recent sympathy for ideas compatible with those of Hameroff’s as an excuse to leech off of the scientific legitimacy of Penrose’s previous work on physics, by simply name-dropping the word “Penrose” and Penrose-related physics ideas (like the Penrose Interpretation) next to their own very unscientific ideas in order to make it appear Penrose himself endorsed those particular ideas directly.

I dunno. Wasn’t this all basically the plot of the later Ender’s Game books? (And Penrose’s latest relevant book was even named “Shadows of the Mind”!)
#113 Jeff L
June 12, 2007

Next I will prove the existence of Odin through numerological references in Beowulf. Well, the Classic Comics version, anyway.

Posted by: kehrsam | June 8, 2007 06:05 PM

There are no references to Odin in Beowulf. The Anglian scribes who wrote down the only copy in existance were Christians.

Don’t know about the Classic Comics version, though.
#114 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi Coin,

Thank you for your thoughtful response.

Actually, I am wary of Hameroff’s claims and I would rather get more information directly from Penrose.

As for the “flamewar” has been pretty much me against everyone else. The IDers aren’t overly thrilled with my ideas either.

I am curious where you think I cross the line from Penrose to Hameroff. I think Penrose’s chain of logic is understandable. Let me summerise…

Penrose and just about everyone else recognises quantum weirdness exists. More formally known as the EPR paradox link

In 1994 Penrose and Hawking had a big debate which was captured in a book titled The Nature of Space and Time The backdrop in the debate was that Penrose was claiming paradoxes like EPR and Schrodinger’s Cat had to be explained whereas Hawking did not. Penrose’s explaination (quantum gravity and waveform collapse) was something Hawking did not want to accept even though he had no other answer that fit the facts.

Hopefully, you don’t have a problem with this. This is old news. Especially to Penrose.

To Penrose, waveform collapse has been a scientific reality for over a decade. The rest of us are now coming around and accepting it. Even Tegmark, one of the biggest critic of Penrose/Hameroff, accepts Penrose’s waveform collapse formula. Tegmark just disagrees that it effects microtubules.

Penrose is a very good mathematician. And he has made a name for himself modeling things that should be impossible to model. If anyone would be able to recognize, and deal with, non-algorithmic things in nature, it would be Penrose.

Have you heard of the Penrose Tilings?. As a background hobby, Penrose figured out a simple two tile solution to the mathematical puzzle of how to tile an infinite plane with no repeating patterns. The solution was named after him.

Penrose claims there is no generalized algorithmic solution to the aperiodic tiling problem. He is claiming his own solution was not algorithmically determined. Therefore, he concluded that human thinking is, at least parially, non-algorithmic.

Armed with this and Gödel’s second theorem, Penrose proceed to mathematically claim that Strong AI was impossible.

Ten years later, quasicrystals were discovered. These crystal formations were thought impossible by mineralogists because they were aperiodic. They matched Penrose Tilings.

Penrose points to this a separate proof that non-algorithmic things are possible in nature. He suggests these natural occurances must tracable back to a primary source. The non-random, non-algorthmic process of waveform collapse at the quantum level,

Here is a slide in a presentation the Penrose gave where he points out a chess problem that is easy for humans to solve, but the algorithmic chess playing computer, Big Blue, could not.

I suggest the Penrose-Hameroff model of tubule dimers is very much in keeping with Penrose’s chain of logic. To Penrose, something physically real is transferring quantum effects into human consciousness. Penrose admits it might not be microtubules, but I think he firmly believes that some mechanism exists.

Provoking Thought
#115 fnxtr
June 13, 2007

TP/QQ:

PLease explain this statement:

the cross-correlation between the two cultures grows up at maximum levels

… and you didn’t answer my other questions:

me:

And what does “The future resonating with the past” mean?

Please be specific.

and me:

Are you seriously suggesting quantum effects have transported post-synaptic protein homologues into the genomes of sponges in the distant past?

… or are in some other way responsible? That DNA grew backwards in time because it was exposed to some quantum effect?

Again, please be specific, and use your own words.

Thank you.
#116 Coin
June 13, 2007

I suggest the Penrose-Hameroff model of tubule dimers is very much in keeping with Penrose’s chain of logic.

But it isn’t. There is no particularly meaningful unifying relationship behind any of the five things:

1. Penrose tilings
2. The details of the “Penrose interpretation” of the quantum mechanics (the unique feature[s] of which, incidentally, as far as I’m aware of is not the idea of waveform collapse)
3. Penrose’s debate with Hawking over the reality or unreality of the waveform and the completeness of quantum physics
4. Penrose’s conjectures about the relationship of quantum physics to consciousness and AI
5. Your entire stream of gibberish about consciousness going backward in time to implant quantum DNA into sea sponges, or whatever

…except that Roger Penrose was involved in four of these things, and you’ve mentioned his name a lot in talking about the fifth. Roger Penrose is surely a very smart person, but it doesn’t follow that you can justify pseudoscience just by repeatedly mentioning that Penrose at one time worked on something distantly related.
What you’ve basically done here is barge in, spew a bunch of nonsense about “retrocausual synaptic development”, and when asked to actually back anything you said up, you instead started endlessly trying to divert attention by talking about uncontroversial but utterly irrelevant stuff like the existence of an EPR paradox and Penrose tilings.
#117 Ed Brayton
June 13, 2007

Coin-

In other words, it’s a bunch of gibberish. I think that’s what I said.
#118 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi Coin,

You wrote…

What you’ve basically done here is barge in, spew a bunch of nonsense about “retrocausual synaptic development…

If Ed tells me to leave, I am gone and I will leave you to your sanctimonious Group Think so you can return to your relaxed state and continue laughing at ideas that make you uncomfortable.

My only agenda is to provoke thought, but all I can do is provoke. I can’t force you to think one way or another. Even if I could, I wouldn’t want to.

I have been honest and, I believe, fairly balanced in my comments.

You said…

You keep invoking Penrose’s name here, and trying to drag in the Penrose Interpretation of quantum mechanics as if it were in some way linked to Penrose’s separate writings on the nature of consciousness. (As far as I know, they’re two separate ideas that just happen to have come from the same person.)

I feel Penrose is sincere in his suggestions and I find it interesting that you want to force a separation of various Penrose ideas as totally unconnected (You aren’t the only one).

Unfortunately, I messed up the links on my last two comments. Let me try again.

Here is the link to a Penrose presentation where he goes through his ideas of philosophically, mathematically and physically (quantum mechanics) and ends with his explanation of how quantum mechanics through microtubules make the brain think…

http://online.itp.ucsb.edu/online/plecture/penrose/oh/05.html

This may still be gibberish, but it is Dr. Rodger Penrose, himself, presenting it at Oxford University. And it is definitely interconnected with all his other work. As physics should be and is.

For those who like words better than pictures, here is a link to a summary of Penrose’s arguments I made on Telic Thoughts….

http://telicthoughts.com/coordinated-evolution/#comment-108797

In fact, looking at the whole thread might be informative.

I need to go to work now. I will check back later to see if you are still interested in thinking, even if it makes you uncomfortable to do so.

Provoking Thought
#119 harold
June 13, 2007

Thought Provoker or Provoking Thought –

You wrote –

“DNA and microtubules are small enough to directly experience quantum effects.”

This is a matter of semantics, to some degree, since one could make the facetious (but technically true) argument that the entire universe is small enough to “directly experience” quantum events – just an overwhelmingly incomprehensible number of quantum effects in even the most infintesimal period of time.

However, in standard scientific usage, it is essentially wrong. DNA and microtubules are relatively large structures, composed of macromolecular builing blocks –

http://en.wikipedia.org/wiki/Microtubule

Perhaps you were unaware of the scale of biological macromolecules. It’s an excellent idea to keep scale in mind. When dealing with microtubules, tubulin, or even the amino acid molecules that bond to form tubulin molecules, we are dealing with structures that are tens of orders of magnitude more massive than photons, electrons, quarks, and the like. Indeed, there are plenty of viruses with a diameter similar to the diameter of a microtubule. Quantum mechanics is potentially relevant to molecular biology and biochemistry, but no more so than it is to other fields that deal with structures that effectively behave on a Newtonian scale, such as much of chemistry, astronomy, geology, mechanical engineering, and so on.

Also, like many, you seem to be strongly interested in the idea of randomness.

You will notice that I did not use the word “random” in my summary of the theory of evolution, or even “mutation”, let alone any terms like “accidental”. It is often said the variations in offspring genomic sequence that occur during replication (relative to parent genomic sequence), “mutations” if you will, are “random”, and this is true when understood correctly. They are random with respect to what their future impact will be, the neutral and “bad” happen as well as the “good”.

Actually, I prefer to use a better mathematical term for this relationship. Genetic variations in offspring genomes are independent of human-perceived “needs” or “wants” of the parent organism.

http://en.wikipedia.org/wiki/Statistical_independence

As for the philosophical implications of quantum mechanics, that is in some ways an interesting topic, although one I won’t get into here, but there is no interpretation of quantum mechanics that casts any doubt onto the theory of evolution of biological organisms on earth.
#120 John
June 13, 2007

TP wrote:
“I may be confused, but I found this which includes…”

You are very, very confused. The subject of the sponge genome paper was the group of proteins that function in mature synapses. The blurb you found below is about the steps that precede it (synaptogenesis). If you would have looked at the diagram instead of searching for a quote to mine, my point would have been obvious.

Since you’re partial to ID, here’s an analogy: growth cone migration is like an amoeba (the growth cone) on a leash (the axon). The axon is chock-full of microtubules (MTs), which obviously have to be plastic to allow the amoeba to search for a place to form a synapse (if it does, there’s retrograde signaling from the synapse to tell the neuron to stay alive, otherwise it undergoes programmed cell death, which is selection, not design).

The reason your statement was gibberish is that the MTs end before the synaptic region, whose cytoskeleton is mostly actin. This was shown in the diagram that you ignored in your defensiveness.

“How does being “actin-rich” translate into “no microtubules”?”

It doesn’t, but there has to be some cytoskeletal scaffolding. I was anticipating such a challenge.

Here’s some advice: don’t believe anything Joy says about biology, especially when it involves well-known facts. Would you believe her or someone who has a [minor] publication record in identifying proteins of the postsynaptic density?
#121 John
June 13, 2007

To clarify, it should be, “The subject of the sponge genome paper was the group of proteins that function PHYSIOLOGICALLY in mature synapses. The blurb you found below is about the DEVELOPMENTAL steps that precede it (synaptogenesis).”
#122 Coin
June 13, 2007

My only agenda is to provoke thought, but all I can do is provoke.

You can’t inspire what you don’t practice
#123 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi John,

First of all, thank you for responding and being at least somewhat tolerate my bumbling.

You wrote…

Here’s some advice: don’t believe anything Joy says about biology, especially when it involves well-known facts. Would you believe her or someone who has a [minor] publication record in identifying proteins of the postsynaptic density?

And I suspect Joy would advise me against believing anything a dogmatic biologist says about quantum mechanics.

I readily admit I am much more comfortable with quantum mechanics (I’m an engineer) than I am with wiggly squiggly things with overly complicated names.

I also can generally hold my own in mathematics.

I need to understand something in order to believe it. Whether Joy, you or anyone else, I won’t accept a conclusion without understanding the evidence and logic that leads to that conclusion.

I also like to argue. So I plop myself down in the middle of a hostile environment and let others explain where I am “confused”. As you can probably imagine, this has made for some interesting conversations at Telic Thoughts.

It forces me to think about what I think.

At this point I am willing to concede that I don’t have a strong case for suggesting the sponge genome paper provides evidence of retrocausality. I will have to try harder.

Meanwhile, what is your thoughts about the Penrose-Hameroff model concerning microtubules in general?
#124 harold
June 13, 2007

Thought Provoker –

Although you didn’t bother to reply to my comments on the scale of microtubules, I did find a link with a summary of Penrose Hameroff.

http://www.starlarvae.org/Star_Larvae_The_Physics_of_Subjectivity.html

As far as I can tell, it has nothing to do with ID/creationism/evolution denial

It is, in fact, one of many fascinating yet, for now, poorly testable hypotheses about the generation of consciousness.

I would personally question that consciousness is related to a ubiquitous cellular organelle like the microtubule.

I offer no explanation of consciousness, but I do know that human states consciousness seem to depend, physically, on the physical states of the brain. Therefore, I would suggest that human consciousness (and the consciousness of other obviously aware mammalian species) is related to the brain. Of course the brain has microtubules, but they don’t seem to be a unique and defining feature of it.
#125 Ed Brayton
June 13, 2007

Thought Provoker wrote:

If Ed tells me to leave, I am gone and I will leave you to your sanctimonious Group Think so you can return to your relaxed state and continue laughing at ideas that make you uncomfortable.

No, I have no desire to tell you to leave. But I will point out that it’s hardly “sanctimonious” for people to point out that your ideas are totally incoherent nonsense.
#126 John
June 13, 2007

TP wrote:
“And I suspect Joy would advise me against believing anything a dogmatic biologist says about quantum mechanics.”

Well, if you’re referring to me, I’m not saying anything about quantum mechanics. If you think I’m dogmatic, you’re clueless, because the only scientific projects that excite me are those that bust dogma in the teeth. Do you realize that there is a lot of dogma in cell biology that is based on our human tendency to view things as designed, that the data rarely support such telic notions, and that this poses a barrier to scientific progress?

What’s the primary biological function of something called a “molecular motor” that moves along actin or MT tracks, for example?

“I readily admit I am much more comfortable with quantum mechanics (I’m an engineer) than I am with wiggly squiggly things with overly complicated names.”

MTs are remarkably straight. The actin filaments are the wiggly-squiggly ones.

“I need to understand something in order to believe it. Whether Joy, you or anyone else, I won’t accept a conclusion without understanding the evidence and logic that leads to that conclusion.”

OK, so what is the evidence underlying the Penrose-Hameroff model? Has it predicted anything empirically?

“Meanwhile, what is your thoughts about the Penrose-Hameroff model concerning microtubules in general?”

It looks to me as though someone with a mathematical bent read a paper 13 years ago with mathematical descriptions of tubulin polymerization/depolymerization and quit looking further. I don’t see any evidence that suggests that it is more likely to be true than the idea that consciousness is an emergent property of neural networks, driven by long-term potentiation (in which actin, not tubulin, plays a supporting role).

What do people who have studied MTs for entire careers think about it? If any true experts would be biased in favor of it, it would be them!
#127 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi Harold,

I am sorry that I didn’t get back to you right away. Your comments and reactions are similar to what I would be doing if our roles were reversed. I am impressed that you took the effort to look for yourself what I was babbling about.

Yes, you are correct. I am stretching Penrose-Hameroff further than intended, but I would disagree that “…it has nothing to do with ID/creationism/evolution denial”.

First of all, the Cambrian Evolutionary Explosion comes up in this debate quite often. Here is Hameroff’s treatment of that…
http://www.hameroff.com/penrose-hameroff/cambrian.html

While Penrose-Hameroff must be somewhat gentle with its claims, I do not. Retrocausality is a practically a given at the quantum level. There is no reason to arbitrarily decide something that is unlimited in effecting all of space in space-time is somehow limited in effecting all of time. It explains too much to consider the universe as one big pre-determined interconnected system that forces internal consistency via the “non-deterministic” quantum effects.

Yes, this makes me a quantum quack. But at least, I believe, my logic has internally consistent. Unlike most ID hypotheses.

Provoking Thought
#128 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi Ed,

Thank you for being tolerant of this use of your Blog.

For what it is worth, I think you bring up some very interesting subjects and present them well. Unfortunately, I agree with most of them. It’s no fun just agreeing. I like to argue.

Hopefully, my stay here has provided you with some entertainment.
#129 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi John,

You wrote…
“MTs are remarkably straight. The actin filaments are the wiggly-squiggly ones.”

LOL. I’m glad to see you have a sense of humor.

You asked…
“OK, so what is the evidence underlying the Penrose-Hameroff model? Has it predicted anything empirically?”

Well, kind of. There is this experiment…
http://adsabs.harvard.edu/abs/2004SPIE.5436..107P

In recent times the interest for quantum models of brain activity has rapidly grown. The Penrose-Hameroff model assumes that microtubules inside neurons are responsible for quantum computation inside brain. Several experiments seem to indicate that EPR-like correlations are possible at the biological level. In the past year , a very intensive experimental work about this subject has been done at DiBit Labs in Milan, Italy by our research group. Our experimental set-up is made by two separated and completely shielded basins where two parts of a common human DNA neuronal culture are monitored by EEG. Our main experimental result is that, under stimulation of one culture by means of a 630 nm laser beam at 300 ms, the cross-correlation between the two cultures grows up at maximum levels. Despite at this level of understanding it is impossible to tell if the origin of this non-locality is a genuine quantum effect, our experimental data seem to strongly suggest that biological systems present non-local properties not explainable by classical models.

But you bring up an interesting point. Why microtubules and not actin? Harold was correct when he said “…one could make the facetious (but technically true) argument that the entire universe is small enough to “directly experience” quantum events.”

I am mostly clueless on how to close the loop. But it is becoming scientifically accepted that consciousness (observation) plays a role in waveform collapse. Although the implications are totally weird they are reality.

The engineer is telling me that somehow, someway the consciousness/quantum loop has to be closed or the universe doesn’t make sense.

Thank you for your indulgence. I also thank you for giving me more to think about.
#130 John
June 13, 2007

TP,
What does that experiment have to do with microtubules?
#131 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi John.

You asked…
“What does that experiment have to do with microtubules?”

That was the “kind of” part. Even though the researchers indicated they were testing for non-local quantum effects in microtubules in the brain, their experiment wasn’t limited to just microtubules, but included everything in a “human DNA neuronal culture”. The quantum effect could have come from actin filaments for all they know.

However, if you accept the experiment’s validity and the researchers interpretation that the “…data seem to strongly suggest that biological systems present non-local properties not explainable by classical models”, then something is happening. Would you rather consider this supporting evidence for E.S.P.?

As for me, I will stick with a scientific property that has been experimentally demonstrated countless times since 1930s.
#132 harold
June 13, 2007

TP –

A final comment.

First of all, you state –

Yes, you are correct. I am stretching Penrose-Hameroff further than intended, but I would disagree that “…it has nothing to do with ID/creationism/evolution denial”.

Well, sort of. The article you link has an advocate of P-H proposing their model, which however eccentric and untestable at present, is clearly grounded in, and does not appear to yet outright contradict, accepted science, as a contributing factor to the “Cambrian explosion”. (I’m going to use that terminology, and it has a meaning, even though it is sometimes seen as an oversimplified term).

This is the exact opposite of the ID position on the “Cambrian Explosion”. P-H accept the fossil record and propose a physical, if eccentric, contributing factor to evolution (as a corollory, they seem to believe that marine invertebrates possess “consciousness”). The ID position is that either the Cambrian Explosion did not happen because the earth is 6000 years and fossils are remnants from Noah’s flood (in private) or that the Cambrian explosion happened but magic was required (in courtroom testimony and in some other public venues). P-H has something to do with ID in the sense that specifically rejecting ID is having something to do with ID.

You also state –

Retrocausality is a practically a given at the quantum level.

The key word here is “practically”. I could dwell on whether this is true, but the salient point is that whether true or not it has no more to do with evolution or microtubules than it does with anything else.

In my first post, I pointed out that the term “intelligent design” causes confusion. You seem to be a person who is interested in thinking about quantum mechanics, and drawing conclusions about philosophy and consciousness. The perceived quality of your conclusions notwithstanding, that is not an inherently unreasonable thing to do.

Unfortunately, you seem to mistakenly believe that the theory of biological evolution has something direct to do with these topics. It does not, although there is some potential overlap with each. The current theory of evolution is primarily grounded in the interaction of biological molecules and larger structures with one another and the surrounding environment; we might compare the scale it studies as ranging from that of organic chemistry to that of mechanical engineering. It is worth learning about in itself, and I recommend that you purchase standard textbooks on biochemistry, organic chemistry, general biology, molecular biology, cell biology, genetics (which presumably now includes what is now known as “genomics”), population genetics, and perhaps neurobiology if you are so inclined. I assume, since you refer to yourself as an engineer, that you are already familiar with general physics, general chemistry, basic statitics, and mathematics at least to the level of rigorous freshman calculus. You may learn a lot about microtubules that way, but you won’t learn much about retrocausality.

The “Intelligent Design”, as now used, most certainly does not include any religious philosophy that conceives of any purposeful or intelligent supernatural force interacting with the universe, that would border on making me an advocate of a weak form of it myself. Rather, it refers to a very specific, very stupid, politically motivated form of evolution denial practiced by the fellows of the Discovery Institute and a few other charlatans.

For the record, I doubt that microtubules, which have almost certainly existed since long before the Cambrian Explosion, are especially related to consciousness. Of course, I could be convinced otherwise by empirical data, although it’s hard to see how such data could be generated at present.
#133 Thought Provoker (aka Quantum Quack)
June 13, 2007

Hi Harold,

I am sorry if I gave you the impression that I had anything but contempt for the ID Movement and its leaders. However, I believe some people who call themselves ID proponents are earnestly searching. Yes, they are rather obvious in what they are searching for, God, but some really do want to do the science.

In case it wasn’t obvious, I am considered an ID critic by most people. As you pointed out, Penrose/Hameroff would be detrimental to typical ID hypotheses. What I am proposing as an overall hypothesis would be downright devastating. Imagine an explanation for “design” that does not support the existence of God. Plus, as a bonus, the elimination of the concept of Free Will.

All this because “We followed the evidence wherever it led”.

It’s time for the next paradigm shift. For the record, I think Penrose is on to something even if the details are fuzzy right now.
#134 John
June 14, 2007

“Yes, they are rather obvious in what they are searching for, God, but some really do want to do the science.”

NONE of them want to do the science. ID is all apologetics. The fear of putting their hypothesis to the test shows an absence of faith. For real scientists, our enthusiasm for trying to falsify our own hypotheses is proportional to the faith we have in them.

That is the single most striking aspect of the ID movement.
#135 straight talk
June 14, 2007

Equally as important, while front loading presumes that those genes serve no function before they are later expressed, exaptation predicts that they must have some function if they are highly preserved over a long period of time. They simply must be expressed in the phenotype for some function or they will mutate in to uselessness. And that is exactly the case here, as this study found that those genes, though virtually identical between sponges and humans, serve a different function in sponges than they do in humans (obviously so, since the sponges have no nervous system).

Unless the function of these genes in sponges has actually been identified, this is a circular argument. In fact, the study didn’t find that the genes “serve a different function”, it didn’t identify their function at all, it only established their presence.

I have no doubt that the genes do serve a function (and therefore obviously a different one than in humans), due to the “mutate into uselessness” argument, but “that is exactly the case here, as this study found that those genes, though virtually identical between sponges and humans, serve a different function in sponges than they do in humans” is simply false.
#136 straight talk
June 14, 2007

For the record, I think Penrose is on to something even if the details are fuzzy right now.

For the record, Penrose was thoroughly refuted years ago by numerous cognitive scientists, AI experts, logicians, and mathematicians, including his own mathematical mentor, Sol Fefferman.
#137 straight talk
June 14, 2007

But it is becoming scientifically accepted that consciousness (observation) plays a role in waveform collapse.

Consciousness has nothing to do with observation in the physical sense; an observation is the taking of a measurement, which doesn’t require any consciousness. And just what does “scientifically accepted” mean? Just because something is accepted by some number of scientists does not imply that acceptance was a result of the scientific method. There’s a lot of conceptual confusion about “waveform collapse”, and the popularity of this or that interpretation is neither here nor there scientifically.
#138 straight talk
June 14, 2007

I also like to argue. So I plop myself down in the middle of a hostile environment and let others explain where I am “confused”.

The technical term for that is “trolling”.
#139 Thought Provoker (aka Quantum Quack)
June 14, 2007

Hi Straight Talk,

You wrote…

The technical term for that is “trolling”

I believe you are correct.

Thank you for your response and information. You have given me some things to think about. Meanwhile…

Time will tell if Sir Rodger Penrose has been “thoroughly refuted”. I agree he has made mistakes and things are still fuzzy.

I am curious, since you appear to believe Penrose’s model is wrong, what is your answer to the Schroedinger Cat paradox?

I know of two alternative responses…
1. Ignore the paradox and hope it will resolve itself
2. Explain it with multiple universes

Or are you suggesting that even if Penrose’s Objective Reality model is not scientific, it might be useful?

Description from Wikipedia…

The threshold for Penrose OR is given by the indeterminacy principle E=ħ/t, where E is the gravitational self-energy (i.e. the degree of spacetime separation given by the superpositioned mass), ħ is Planck’s constant over 2π, and t is the time until OR occurs. Thus the larger the superposition, the faster it will undergo OR, and vice versa. Small superpositions, e.g. an electron separated from itself, if isolated from environment would require 10 million years to reach OR threshold. An isolated one kilogram object (e.g. Schrodinger’s cat) would reach OR threshold in only 10-37 seconds. Penrose OR is currently being tested.

It is my opinion that testing a quantifiable hypothesis is appropriately called “science”.

Of course the implications of this science might be uncomfortable for some people. Wikipedia continues with…

An essential feature of Penrose OR is that the choice of states when OR occurs is selected neither randomly (as are choices following measurement or decoherence) nor completely algorithmically. Rather, states are selected by a “non-computable” influence involving information embedded in the fundamental level of spacetime geometry at the Planck scale.

http://en.wikipedia.org/wiki/Orch-OR