That's a sponge? You've got some nerve.
by BradfordOrigin of Nerves Traced to Sponges contains this predictable, indeed, seemingly obligatory line:
A new study has surprised researchers, however.
Let's get the unsurprising surprised reaction stated at the outset and go for the meat:
"We are pretty confident it was after the sponges split from trunk of the tree of life and sponges went one way and animals developed from the other, that nerves started to form," said Bernie Degnan of the University of Queensland. "What we found in sponges though were the building blocks for nerves, something we never expected to find."
This pattern has become so commonplace one is tempted to ascribe a template formula for research labeled under the front loading tab. Find trunk splits and begin a search for biological building blocks. I know. This is all predicted by mainstream evolution. Except for the surprise part. More:
"But what was really cool," he said, "is we took some of these genes and expressed them in frogs and flies and the sponge gene became functional — the sponge gene directed the formation of nerves in these more complex animals.
This is nerd heaven.
August 31st, 2008 at 9:42 am
Bradford:
Thanks I’ve been waiting for someone to post this finding.
From the article:
quote:
the sponge gene directed the formation of nerves in these more complex animals.
end quote
The question I have is what are these genes doing in the sponge? Are they expressed? Do they perform a secondary non neuron function? Someone needs to do a knock out experiment asap. I’m interested to know if this result supports Mike Gene’s Hypothesis or Michael Sherman’s.
It’s getting easer and easer to claim ID is science after all.
No matter which ID Hypothesis this finding supports in the end it is sure to be explained away by yet another epicycle from MET .
Peace
Comment by fifth monarchy man — August 31, 2008 @ 9:42 am
August 31st, 2008 at 10:10 am
Some findings are amenable to follow-up research. Anomalies can be fertile ground for evidentiary support of new theories.
There are, broadly speaking, two types of critics. Some make valid points even if unconvinced that ID can have viability because their critiques stick closely to evidentiary norms. Then there are others whose response is always a variation of show me God and then we'll talk. Discussions with the latter faction are wasteful.
Comment by Bradford — August 31, 2008 @ 10:10 am
August 31st, 2008 at 2:48 pm
Here's what apparently happened: gene X was present before the split between sponges and animals. In animals, X now plays a role in triggering neuronal development. In sponges we don't know, but it certainly doesn't trigger neuronal development. We also don't know what X was doing, if anything (perhaps it was "hibernating"), in the common ancestor of sponges and animals. Agreed?
According to FL, as far as I can follow its logic, the designer(s) inserted or mutated X into the genome, knowing/suspecting/guessing that at some point during evolutionary history it might trigger neuronal development. Thus, an important foundation for brains, intelligence, humanity and potential divine incarnations has been laid.
However, the plan was not without flaws, since X failed to evolve triggering of neuronal development in sponges. Apparently, it's not an easy task to predict what will happen when you frontload a new gene (unless stupid sponges were part of the plan). I call this type of frontloading, where X evolves only part of the time the function that was intended, type II frontloading.
Of course there is also type I frontloading. Suppose X had been frontloaded after sponges branched off and it would also have evolved its current function. In a sense it would have been a more successful act of frontloading since it evolved according to plan 100%.
What surprises me is that you cry "frontloading!" whenever you think you see evidence for type II frontloading, but never when there is evidence for type I frontloading (in effect, any time an important gene is discovered that does not have different functions in different lineages). Can you explain why? Or am I reading this incorrectly?
PS I hope you won't go all pugilistic on me this time.
Comment by Raevmo — August 31, 2008 @ 2:48 pm
August 31st, 2008 at 4:13 pm
As sponges may have diverged *after* Ctenophora, and as Ctenophora have a primitive sub-epidermal nervous system, this is not so surprising after all.
Broad phylogenomic sampling improves resolution of the animal tree of life, Nature 2008.
In any case, we would expect some precursor to the genes involved.
Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit, Current Biology 2008: the bilaterian neurogenic circuit … was functional in the very first metazoans and was used to generate an ancient sensory cell type.
Comment by Zachriel — August 31, 2008 @ 4:13 pm
August 31st, 2008 at 4:24 pm
Zach:
I never cease to be amazed by your lack of surprise. Perhaps you should be sharing your vast predictive ability with actual researchers instead of us.
Unlike you they seem to be very surprised.
Quote:
"What we found in sponges though were the building blocks for nerves, something we never expected to find."
End quote:
Peace
Comment by fifth monarchy man — August 31, 2008 @ 4:24 pm
August 31st, 2008 at 4:47 pm
Zachriel:
Zachriel, invariably these types of links cite surprise on the part of researchers. And just as predictably there is a comment or two indicating no reason for surprise. Why the dichotomy?
Comment by Bradford — August 31, 2008 @ 4:47 pm
August 31st, 2008 at 4:51 pm
Hi Bradford,
Thanks for the thread. It is the kind of presentation that shows a serious attempt at making a serious ID argument.
Ironically, these kinds of attempts can engender more creative and detailed attempts at arguing against it. I hope you will recognize this as a positive even if it initially makes it more difficult to carry on.
I tend to double check popular press articles. In this case it really wasn't necessary. This has been old news and the article appears to be accurately describing it. However I found a scientific research article that goes into more detail, titled The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans
(emphasis mine)
What I was looking for was the suggested explanation for the gene's early presence and extraordinary conservation.
Here is what I found….
The link I provided is to an cached HTML version. It has a link to the PDF version which contains a lot of good graphs and charts. It is a much longer download but I suggest it might be worth the effort to read the PDF version in detail.
I will be.
P.S. to Raevmo, I'm glad to see you are still contributing. I hope you continue to do so.
Comment by Thought Provoker — August 31, 2008 @ 4:51 pm
August 31st, 2008 at 4:58 pm
Consider this claim: All people have had biological parents. Now consider that we wish to determine historical ancestry. We might be surprised that children of Sally Hemings were fathered by Thomas Jefferson. This doesn't call into question the basic mechanism of heredity. But it certainly can be surprising. It certainly surprised some in the Monticello Association.
Biologists are attempting to reconstruct hereditary relationships from hundreds of millions of years ago, often with very little evidence. There have been many surprises.
Comment by Zachriel — August 31, 2008 @ 4:58 pm
August 31st, 2008 at 5:35 pm
TP:
Thank you, I probably will continue, as long as the frequency of getting posts deleted is o(epsilon).
Good luck with becoming one of the "bosses" here. It would be good for TT.
Comment by Raevmo — August 31, 2008 @ 5:35 pm
August 31st, 2008 at 6:03 pm
Zach:
So you are saying that you are not at all surprised that these genes have not been expressed to make nerves for hundreds of millions of years yet when they are placed in organism with a nervous system they become functional?
You criticized my hibernation mechanism prediction because you said such a thing was unstable over deep time yet you are not surprised that viable genes for nerves can survive since the Cambrian with out any protection against mutation at all.
How odd
Peace
Comment by fifth monarchy man — August 31, 2008 @ 6:03 pm
August 31st, 2008 at 6:35 pm
No. I said it was not *so* surprising, especially considering porifera diverged after ctenophora.
Evolution works by modifying what exists. On a molecular level, mechanisms which are established early may be kept, but then modified by layers of later regulation. For example, evolution might establish developmental segmentation, then over time, particular segments become specialized. That results in the original genes being under strong purifying selection, because any change disrupts numerous systems depending on those genes.
Comment by Zachriel — August 31, 2008 @ 6:35 pm
August 31st, 2008 at 6:38 pm
Hi All,
Some select passages from the research paper I found…
http://64.233.179.104/scholar?...
There is something very notable about Runx3…
(emphesis mine)
I will admit that I am still stuggling with the terms and concepts of the paper, but the sense I get is that the proteins that give life awareness and consciousness can be directly traced back to the tree of life's main trunk.
Comment by Thought Provoker — August 31, 2008 @ 6:38 pm
August 31st, 2008 at 6:56 pm
Question for those suggesting the reason for this is due to sponges following Ctenophora…
Why is the nerve manufacturing function so well conserved?
If my math is right, this allegedly useless function was preserved in sponges for a billion years.
Just a coincidence?
All life appears to be more aware than can be reasonably explained. Computer technology is approaching the supposed computing power of the human brain. But I suggest we aren't even close to demonstrating human-like artificial intelligence.
Hypothesis…
All life is interconnected to the universe's quantum wavefunction. It is an efficient means to an awareness helpful in self preservation and, therefore, is ultraconserved in all life, including sponges.
Comment by Thought Provoker — August 31, 2008 @ 6:56 pm
August 31st, 2008 at 7:33 pm
TP:
I don't think you really have to go all the way to the whole universe, TP. We didn't have any idea there WAS a whole universe for all but about a century of our total existence, squirrels and polar bears still don't care. The only "web of life" we know of or have any evidence to support exists here, now and about 3.5 billion years into the past of here and now. If life is hooked in to a forever-collapsing wavefunction, it's peculiar to life and it's confined to here. Now. Until and unless we discover otherwise, in which case we may find that THAT life is on its own wheel of karma.
Just a thought…
Comment by Joy — August 31, 2008 @ 7:33 pm
August 31st, 2008 at 8:11 pm
TP,
Dendritic cells are components of the immune system that specialize in presenting antigens (in us). You're confusing "dendritic" with the dendrite of a neuron. It's just a morphological term.
Comment by richcheese — August 31, 2008 @ 8:11 pm
August 31st, 2008 at 8:15 pm
Can someone parse this for me? I have no idea what Bradford is trying to convey in this sentence.
Comment by richcheese — August 31, 2008 @ 8:15 pm
August 31st, 2008 at 8:44 pm
Hi richcheese,
You wrote…
Thank you for the correction. From what I can tell, you are correct.
By way of an excuse, here is an example of why I thought what I did…
link
Both Dr. Hameroff and an ATBC scientist made a big deal of the importance of the role of Dendritic spines to consciousness. Yes, I jumped to the conclusion Dendric cells had something to do with Dendritic spines.
I'll take quantum weirdness over confusing biological semantics anytime.
Comment by Thought Provoker — August 31, 2008 @ 8:44 pm
August 31st, 2008 at 9:06 pm
Hi Joy,
You wrote…
So you want suggest I tone down my radical, progressive thinking and be a little more conservative, now?
You would think my Dendritic Cell/Spine mix up would have a humbling effect. Any bets that's going to happen?
Yes, I have considered the local verses universal aspects of what I am suggesting. I even agree that some kind of inverse cubed law would be an appropriate presumption. I would apply it to both space and time (years and lightyears).
I would love to get to the point of arguing such details. I'm of the opinion that few people understand the significance of the results of the Quantum Delayed choice quantum eraser experiment (future quantum interactions can effect past quantum interactions as long as they are unobserved)
I have been intending on writing a guest host post on this in hopes of getting Oleg to "review" it. I was going to do it this weekend but I had too much fun at the fair.
Comment by Thought Provoker — August 31, 2008 @ 9:06 pm
August 31st, 2008 at 9:10 pm
Zach:
I want to make sure I understand you.
This sounds like yet another frontloading hypothesis in the making.
So if a frontloader put “the building blocks for nerves” into the first cell he could be reasonably confident that they would be there whenever the need for them would arise?
If I’m reading you correctly you believe no HM or even a subordinate function would be necessary at the outset to frontload something like a nervous system. All a designer would have to do is make sure the appropriate genes were present at the beginning and let nature do the preserving.
Should we label this Idea Zach’s frontloading to distinguish it from the two other views?
Peace
Comment by fifth monarchy man — August 31, 2008 @ 9:10 pm
August 31st, 2008 at 9:27 pm
Except that we can show that this is how networks, which grow by preferential attachment, evolve. No foresight required.
Not quite. The genes have existing functions in the ancestor species, and they are adapted as the organism evolves.
Comment by Zachriel — August 31, 2008 @ 9:27 pm
August 31st, 2008 at 9:30 pm
TP:
Oh, heavens no. I'd just play Rafiki to your Simba… "Look harder." Say, right around 40 Hz and a forever-propagating standing wave bound to the planet. Plug "40 Hz" into Hameroff's stuff. You may have overlooked something important… §;o)
Comment by Joy — August 31, 2008 @ 9:30 pm
August 31st, 2008 at 9:49 pm
Except for the foresight to design such networks. A lack of foresight is insufficient. Granted, you can propose such a state exists - it's just scientifically vacuous.
Interesting OP, nevertheless. Quite amazing design in nature - says I, speaking outside the confines of good ol' science.
Comment by nullasalus — August 31, 2008 @ 9:49 pm
August 31st, 2008 at 10:49 pm
Abiogenesis is not the issue in this thread. Once replication is established, the process of evolution, including the conservation of fundamental genetic systems, occurs without agency. Notably, the genes involved are expressed in sponges.
Comment by Zachriel — August 31, 2008 @ 10:49 pm
August 31st, 2008 at 11:41 pm
Who said anything about abiogenesis? The system of evolution itself is replete with wonderful design, as are the laws which allow it to unfold throughout. Again, spoken outside the confines of science.
As for 'without agency', science has no need of such empty conjectures. The process is the process, the mechanisms are the mechanisms, and they happened however they happened. If you'd like to argue agency, the philosophy department is down the hall - they'll be more than happy to discuss your thoughts of design detection there.
Comment by nullasalus — August 31, 2008 @ 11:41 pm
August 31st, 2008 at 11:43 pm
Hi Joy,
I very much remember seeing 40 Hz.
I understood it to be the result of Penrose's E=h/t.
From Dr. Hameroff's Cambrian paper
"…Orch OR predicts involvement of roughly 102 to 103 neurons (interconnected by gap junctions) for rudimentary conscious events. For more intense conscious events, for example consistent with 25 msec "cognitive quanta" defined by coherent 40 Hz activity…"
The repetative 25ms causes the 40Hz signal to be transmitted.
If you are suggesting that the 40Hz is both transmitted and received in a synchronized fashion like a radio waves but via Quantum Mechanics instead of electromagnetics, I wouldn't argue.
I could even see how other worlds might have "randomly" syncronized on a different frequency.
I would love to argue these kinds of details. I need to find time to put together a coherent post. Unfortunately, right now I think I have a flu bug.
(I hope it isn't one of those with increased imipenem resistance.)
Comment by Thought Provoker — August 31, 2008 @ 11:43 pm
August 31st, 2008 at 11:58 pm
Hi All,
Excuse my fever-induced impatience but do we have a counter explanation as to why a nerve producing function was ultraconserved in a sponge?
While I overreached with Dendritic cells, my previous argument still holds. Life that is aware needs sensory nerves.
My suggested hypothesis is that it is ultraconserved in life because it is key to what make organisms alive.
Even an MET argument can be made that it was a very early selected trait. Not only was it selected but its ultra conservation status was also selected. Life wasn't life without it. Whether front loaded or selected billions of years ago it was put in place early.
Comment by Thought Provoker — August 31, 2008 @ 11:58 pm
September 1st, 2008 at 1:19 am
Because it's not a nerve producing function in the sponge–they don't have nerves. Your conclusion is an artifact of the name you are using. If you refer to it by its biochemical function, a transcription factor, your argument vanishes.
Comment by richcheese — September 1, 2008 @ 1:19 am
September 1st, 2008 at 8:32 am
Oh, you mentioned that your statement was scientifically meaningless. Nevermind, then. As this thread is about a scientific paper on sponges, I'll just ignore your comment.
Comment by Zachriel — September 1, 2008 @ 8:32 am
September 1st, 2008 at 10:26 am
TP:
Oh, wow. How'd you give it to me across these here intertubes? I woke up with a fever in the middle of the night and found myself completely lost in my own house (sleeping in the LR because downstairs is still damp from the foot of rain last week, now it's raining again). Had no idea where I was! And every joint in my body hurts…. ARGH!!!
Hope we get better quick.
Comment by Joy — September 1, 2008 @ 10:26 am
September 1st, 2008 at 10:39 am
Hi Joy,
Sorry to hear you aren't feeling well also.
agreed
Comment by Thought Provoker — September 1, 2008 @ 10:39 am
September 1st, 2008 at 11:02 am
Hi richcheese,
Thank you for your comments. You wrote…
Let's find a description we can agree on. From this PubMed paper…
"The data presented here support the presence of a proto-post-synaptic scaffold in the last common ancestor to all living animals. The presence of a large number of post-synaptic genes in the genome of demosponge Amphimedon, the nearly absolute conservation of binding domains and ligands between this sponge and animals with neurons, as well as the expression of a set of post-synaptic mRNAs in the same cell type, suggest the proto-post-synaptic scaffold existed as an assembled functional structure very early in animal evolution."
It is the "nearly absolute conservation" I am focusing on.
Would you at least agree this conservation is surprising?
Comment by Thought Provoker — September 1, 2008 @ 11:02 am
September 1st, 2008 at 11:42 am
As I mentioned above, conservation is a natural consequence of the growth of networks by preferential attachment. Long-established nodes can be very resistant to change because so many other systems depend upon them.
Comment by Zachriel — September 1, 2008 @ 11:42 am
September 1st, 2008 at 12:45 pm
Hey TP,
Your hypothesis is about why and not how these genes are ultrconserved. My suggested hypothesis for why is that a nervous system is necessary for a designer to communicate with his design.
I’m not sure how we can scientifically distinguish between the two options but I’ve got a way we can do it historically.
In any event I’m interested in how the building blocks are ultraconserved do you have a hypothesis for this?
Zach:
I want to be sure I understand you. You said:
And
It looks like you are saying that in order it get a nervous system all a frontloader has to do is frontload the correct gene and let nature take it’s course.
A frontloader could be reasonably confident that his desired outcome would come to fruition eventually if the first cell had the right information.
Am I reading you right? I understand you don’t believe this is what happened but are you saying it could happen that way?
Peace
Comment by fifth monarchy man — September 1, 2008 @ 12:45 pm
September 1st, 2008 at 4:00 pm
The evidence doesn't point to a designer, but to evolutionary processes.
I think that any particular outcome would be very uncertain.
Yes, someone might have seeded the Earth's formation in the primordial nebula, and if we look at the center of the Earth we might find a small, alien gravitional device—or a bag of litter, a discarded alien beer bottle that acted as the initial core of the nascent planet.
Yes, the Earth may be a big computer designed to find the Ultimate Question.
Yes, someone might have tampered with Earth's genomes. Any minor change a billion years ago could have profound effects today. However, it would be very difficult to predict the trajectory without constant intervention.
The evidence certainly doesn't indicate any of these imaginings have scientific validity. We can dream up an infinitude of possible (but not plausible or supported) ideas. Allowing the mind to wander freely can be fun and intellectually stimulating. But in science, these are considered extraneous entities unless and until there is relevant evidence.
It's only an issue for me when people make unsubstantiated scientific claims.
Comment by Zachriel — September 1, 2008 @ 4:00 pm
September 1st, 2008 at 4:11 pm
I never cease to be amused at people who ignore comments by responding to them!
I'm stating outright that philosophy is philosophy, and science is science. And I'm showing you how to not only draw that line properly, but not be an obvious hypocrite while doing so. It's clear you need some instruction in this regard.
I won't expect a response to this, as by your logic we're both ignoring each other's comments.
Comment by nullasalus — September 1, 2008 @ 4:11 pm
September 1st, 2008 at 4:49 pm
Yes, I am aware of the distinction. And a rose is a rose, but I didn't think to bring it up on a thread about sponge evolution.
Let's take a look at my statement again (keeping in mind that it was made during a scientific discussion).
Saying "No foresight required" means that the supposition of foresight in this case is scientifically extraneous. With appropriate definitions, foresight and design can have empirical implications, so the statement is not scientifically vacuous.
Comment by Zachriel — September 1, 2008 @ 4:49 pm
September 1st, 2008 at 5:12 pm
Zach:
but earlier in this very thread you said
These statements seem to contradict one another
Which is it? Is information present early likely to be very resistant to change.
So that you would not be surprised that sponge genes not expresed for neural activity since the Cambrian would produce nerves in a frog.
Or is the likelihood of preservation of the building blocks for nerves “very uncertain”
If something is very uncertain I would expect you to be surprised when it actually happens.
What am I missing?
I would suggest that if MET can account for both the ultrconservation of these genes with no preservation mechanism at all and also make any particular outcome very uncertain, it can simply explain anything and therefore explains nothing.
One last question,
Would you be at all surprised if knockout experiments showed that these genes are not critical for the sponge just like the ultraconserved genes in mice?
Peace
Comment by fifth monarchy man — September 1, 2008 @ 5:12 pm
September 1st, 2008 at 5:25 pm
Zach:
Has anyone on this thread made unsubstantiated scientific claims? It seems to me that we are only speculating on an interesting finding and trying perhaps to develop hypotheses that would be considered scientific.
You don't even think the finding is "so surprising".
If our speculation about it is not an issue for you why are you even posting here?
Again I find your behavior very odd. What am I missing?
Peace
Comment by fifth monarchy man — September 1, 2008 @ 5:25 pm
September 1st, 2008 at 6:00 pm
Funny how this ignoring each other thing works.
And my response is that any reference to foresight or design at all in this case, positive or negative, is scientifically extraneous. We have in front of us details and information about a development path in biological history. Is it indicative of design or foresight? Does it show a lack of design or foresight? Both positions, both suppositions, are outside the scientific realm - they're interesting concerns, important ones, but simply not science. 'I have no need to consider agency to examine this' is as scientifically warranted as 'This finding is entirely compatible with a prospect of agency'. Both interesting questions. Both defensible. Both outside the concern of science.
Comment by nullasalus — September 1, 2008 @ 6:00 pm
September 1st, 2008 at 6:18 pm
(my emphasisis) Aha!
or, in other words imagine
In other words "imaginary"!
Imagination!!!
You've no imagination!
Comment by Alan Fox — September 1, 2008 @ 6:18 pm
September 1st, 2008 at 6:34 pm
Hi Zach,
You wrote…
If I am understanding correctly, you are suggesting that genes selected very early become key nodes upon which other networked nodes build. Something like a support beam holding up other supporting beams. Arguing that it would make it very unlikely to be unselected by random mutations even if it is no longer directly supporting a given function.
Close?
If so, two responses…
1. Aren't you a little bit surprised that in order of priorities, nerves got top billing? Not blood, not organs, but nerves.
2. Currently, the gene for nerves is thought to be relatively new when sponges split off from the tree of life. There shouldn't have been too many other dependents on this relatively new node. Doesn't that make its "nearly absolute conservation" surprising? Maybe suggesting this gene goes even further back into the tree of life?
Comment by Thought Provoker — September 1, 2008 @ 6:34 pm
September 1st, 2008 at 7:16 pm
I thought let's have a look at the original paper in Current Biology. Final part of the Conclusions section:
Awesome. Sponges are less stupid than we thought. I bolded the part because it seems to indicate, albeit speculatively, at least one more front-loading act was required to evolve "real" neurons. Makes you wonder how many of such acts were required to finally evolve an incarnation-worthy creature.
Comment by Raevmo — September 1, 2008 @ 7:16 pm
September 1st, 2008 at 7:40 pm
Hello everyone
I recently came across this blog and have enjoyed reading the perspectives on offer.
Sorry to stray off topic a bit, but on the subject of nerves, consciousness and ID, I have an interest in the philosophical position of panexperientialism (the view that experience is a fundamental and ubiquitous property of nature), and have recently put up a post on my blog re panexperientialism and ID.
Here is the link for anyone interested.
Comment by justin — September 1, 2008 @ 7:40 pm
September 1st, 2008 at 7:50 pm
A particular node may or may not become established. If it does become established, there is no way to determine in advance how it might be modified by new connections. Consider how many different kinds of organisms have neurons. Consider how many more have gone extinct.
Sometimes yes. Sometimes no. What we can predict is a rough scale-free structure. Some nodes will become hubs, though we may not be able to determine which ones in advance. And these hubs will tend to become more rigid due to all the other dependencies. We will see lots of small changes, a few big ones, and very rare revolutions.
They're expressed in everything from sponges to sparrows. In particular, the Notch receptor is expressed during development in subepithelial sponge cells.
That neurogenesis genes are conserved is not news. What is news is that they are found in sponges. However, it may not be so surprising as other, recent research indicates that sponges diverged after organisms which have a primitive nervous system. It's still highly relevant to untangling metazoan evolution.
The mechanism is natural selection.
No. But I would be surprised if they had no function.
You had suggested that this research supports an ID Hypothesis.
Comment by Zachriel — September 1, 2008 @ 7:50 pm
September 1st, 2008 at 7:58 pm
And you apparently ignored my response.
We can scientifically investigate design, such as in archaeology. We can scientifically investigate foresight, such as in forensics.
You must mean Foresight™, not foresight used as a well-defined and empirically meaningful term. If you define Foresight™ as a strictly metaphysical or religious concept without empirical implications, then you are correct; it would be outside the scientific realm.
As I was responding to a scientific question within the scientific realm, you may assume I am using the term in the former sense.
Comment by Zachriel — September 1, 2008 @ 7:58 pm
September 1st, 2008 at 8:21 pm
I responded - I find it lacking.
Putting aside questions of where archaeology or forensics fall in the grand scheme of the "what is science?" debate, those are both fields where the entire paradigm is concerned with design from the outset, and design of non-controversial entities at that. Further, evolutionary biology doesn't concern itself with design or foresight. It investigates what happened and is happening in the biological sphere. 'Did the sponge develop this way according to a designer's plan? Did the sponge develop this way by purposeless happenstance?' both have the same usefulness with regards to that project: Zero. The concern is how the sponge developed, and what state it was in, full stop. The other questions are interesting, even important, but not helpful to this sphere. Not science.
Wonderful - then any reference, positive or negative, to the foresight of such a metaphysical or religious entity is outside the scientific interest. Agreed.
Comment by nullasalus — September 1, 2008 @ 8:21 pm
September 1st, 2008 at 8:24 pm
Yes. But note that we can't always determine which nodes will become important later. This goes back to the relative importance of contingency and determinism.
It will have a function, otherwise it won't be conserved. A beam holding up other beams has a function—unless you don't think your home's foundation is doing anything.
Rapid communication between areas of a multicellular organism are important for coordinated activity. But this evolved in conjunction with other changes, such as the differentiation of ectoderm, endoderm and a digestive chamber. (The circulatory system is not a necessity for very small organisms.)
If sponges diverged after ctenophores, then not so new. Anyway, a neurogenesis gene has an ancestor, too.
The conservation is due to what happens *afterwards*. As to whether it would be this gene or that gene, it may not be possible to know in advance.
More than likely. Remember, about the only evidence we have is in the very, very few lineages that survived to the present day.
Comment by Zachriel — September 1, 2008 @ 8:24 pm
September 1st, 2008 at 8:54 pm
And here I thought my
Discarded Beer Bottle Causing the Collapse of the Solar Nebula Theorywas worthspending billions of dollars investigatingteaching in public schoolspondering.Comment by Zachriel — September 1, 2008 @ 8:54 pm
September 1st, 2008 at 9:34 pm
Hi Zachriel,
Thank you for responding.
I wish I was more versed in biology so I could offer you a better challenge.
Hey, do you want to discuss the implications of the Quantum Delayed Choice, Erasure experiment using Minkowskian to Twistor Space geometry transformations?!?!?
Ok, maybe that would be off-topic for this thread.
Comment by Thought Provoker — September 1, 2008 @ 9:34 pm
September 1st, 2008 at 10:50 pm
Zach:
quick question, would you call Michael Sherman's idea a Hypothesis?
If not why not?
this statement explains alot
It might be a good idea to relax. Not everyone is out to cut your funding and teach the Catechism to fifth graders.
At least not yet
I am genuinely interested in what you have to say and I respect your expertise but if your every comment is shaped by fear of giving away too much to the fundies it makes it hard to take you seriously.
Peace
Comment by fifth monarchy man — September 1, 2008 @ 10:50 pm
September 2nd, 2008 at 3:07 am
TP,
1) There's no such thing as a "PubMed paper." It's an abstract–it looks like you haven't bothered to read the paper.
2) "It is the "nearly absolute conservation" I am focusing on." No, you're focusing on the label and confusing it with function (transcription factor).
3) "Would you at least agree this conservation is surprising?" Not very. Besides, if something is surprising, how do you infer design from that?
4) "Aren't you a little bit surprised that in order of priorities, nerves got top billing? Not blood, not organs, but nerves." Why do you claim that nerves got top billing? Why not neurons? Do you know the difference between nerves and neurons? Why not transcription factors?
5) "… the gene for nerves…" It's a transcription factor, not a "gene for nerves." You're assuming design. If some intellligence had designed a "gene for nerves," wouldn't you predict that you'd only find it expressed in nerves? And in which component of the nerves, neurons or glia, would you predict it would be expressed in?
Comment by richcheese — September 2, 2008 @ 3:07 am
September 2nd, 2008 at 7:59 am
Instead of taking it as a challenge, why not try to understand my point? You might also absorb what richcheese is saying roundabout.
Loosely. No one doubts that many developmental genes were established early in metazoan evolution. Let's look at Sherman's closer.
That's funny. Sea Urchins have chemical and light sensitive receptors on their body surfaces and tube feet. I suppose if a scientist blinded them, they would still be viable.
Now, think about an alien who knows very little about human physiology, blinds them with a heat-ray and allows them to reproduce in its lab. Then reports in the Journal Xenobiology, "very surprising how deleting those organs doesn't seem to affect their viability".
Comment by Zachriel — September 2, 2008 @ 7:59 am
September 2nd, 2008 at 10:27 am
Richcheese wrote:
The surprise stems from the fact that standard evolutionary theory expects innovation, whereas the front-loading hypothesis expects "deep borrowing". We keep getting examples of the latter, thus supporting the hypothesis.
Comment by Guts — September 2, 2008 @ 10:27 am
September 2nd, 2008 at 10:32 am
Zachriel:
As I have shown previously , many properities of biological networks are in fact not just a "natural consequence" of a certain type of mechanical growth. Another example, mathematical models predict that in a growing network the efficiency will be decreased. But it has been demonstrated the opposite is true in biological networks. It is likely that it is the properties of the network itself, (e.g. special rate of nodes and edges) , and other mechanisms in play, (e.g. gene duplication). It is the evolutionary constraint on these networks itself which might cause even the preferential attachment phenomena and other features of the networks (scale freeness).
Comment by Guts — September 2, 2008 @ 10:32 am
September 2nd, 2008 at 11:02 am
Evolutionary theory expects mostly small modifications of existing structures. Innovation is often only recognized after long periods of evolutionary change. From the broad historical view we may see fins to legs to arms to wings, but birds are still tetrapods.
After all, humans are 'just' elaborated Deuterostomes. A tube with appendages to stuff food into one end. Microevolution.Comment by Zachriel — September 2, 2008 @ 11:02 am
September 2nd, 2008 at 11:07 am
Zachriel:
No, it is only recently , due to the accumulation of the data such as in the OP , that it is now thought that evolution works through slight modification of ancient structures. Many times it was expected that most features arose independantly. Which is why they keep using the word "unexpected". This has all been explained to you before.
Comment by Guts — September 2, 2008 @ 11:07 am
September 2nd, 2008 at 12:05 pm
And here I had read somewhere that Darwin proposed gradual modification of existing structures. That an ancient structure, such as a limb, might be "recycled, recombined, repurposed, or otherwise modified for new uses", such as a wing, or a hand to make and use tools.
Comment by Zachriel — September 2, 2008 @ 12:05 pm
September 2nd, 2008 at 12:22 pm
Zachriel:
Existing structures yes. That these existing structures already existed in ancient ancestors (at times in an already complex state), and moreso because there was optimization by gene loss, is what is surprising modern evolutionary biologists and supporting the hypothesis of Front-Loaded Evolution.
Comment by Guts — September 2, 2008 @ 12:22 pm
September 2nd, 2008 at 12:32 pm
Undoubtedly. Nor did I claim that any mathematical model completely describes biological systems. However, network models based on gene duplication and divergence have shown good agreement with protein networks.
Comment by Zachriel — September 2, 2008 @ 12:32 pm
September 2nd, 2008 at 12:39 pm
You are not drawing the distinction. Darwin proposed that structures, such as fins on fish have been "recycled, recombined, repurposed, or otherwise modified for new uses". Fins are certainly complex and ancient structures.
Comment by Zachriel — September 2, 2008 @ 12:39 pm
September 2nd, 2008 at 12:52 pm
Zachriel:
Of course I am. I'm drawing the distinction between:
and
Zachriel:
That these structures are ancient is irrelevant. The distinction is that the structures from which fins draw from are , much, much older, older than anyone expected. Darwin, or anyone after him, never fathomed that the genes necessary to build a multicellular body plan already existed in single celled organisms.
Comment by Guts — September 2, 2008 @ 12:52 pm
September 2nd, 2008 at 12:55 pm
Zachriel:
You're forgetting horizontal gene transfer, which introduces foreign nodes to an existing network and is known to be rampant in bacteria and is regarded as a major force in bacterial genome evolution. Bacterial network system, can thus rely on mechanisms independent of the duplication-divergence model to evolve their networks and gain new functions.
Comment by Guts — September 2, 2008 @ 12:55 pm
September 2nd, 2008 at 1:42 pm
Evolutionary theory would predict that fins are adaptations of even more ancient structures.
Just because a single model doesn't examine every aspect of biological evolution doesn't mean it doesn't demonstrate important facets of the process. Maybe some specifics will help.
I'm not forgetting horizontal gene transfer. Along with network size and environmental diversity, horizontal gene transfer helps explain the evolution of modularity.
Comment by Zachriel — September 2, 2008 @ 1:42 pm
September 2nd, 2008 at 1:49 pm
Zachriel:
In fact, during Darwin's time, the link between fins and limbs seemed impossible. It wasn't until 1988 that the link , surprisingly, was beginning to be established.
And no, evolutionary theory does not predict such examples, otherwise, researchers wouldn't be thinking they are looking at a unique structure, but then be utterly surprised when they find that it existed in ancient organisms, more ancient than they ever fathomed.
But at this point of course, you're just going to keep repeating yourself.
Zachriel:
My point of course, is that to accurately describe complex biological networks, you need to include multiple facets,many of which are currently not known.
Comment by Guts — September 2, 2008 @ 1:49 pm
September 2nd, 2008 at 2:26 pm
We can see from this study that transcription regulation genes seem to be well suited to control neural development later in evolution. And this of course is apparently what facilitates consciousness. But let's look earlier.
Convergent Evolution of Gene Circuits, Conant and Wagner, Nature Genetics July 2003, Volume 34, Number 3, pg. 264-265.
Transcription regulation circuits evolved independently, largely due to optimal design. Transcription regulatory gene circuits seem to be a foregone conclusion given the optimal design of the genetic code.
There's still dots to connect, but it appears that the capacity, and even the tendency towards consciousness appears not just in the metazoan trunk of life, but at the establishment of the code itself.
Should I be surprised? Or is this once again exactly what MET predicted?
Comment by chunkdz — September 2, 2008 @ 2:26 pm
September 2nd, 2008 at 2:26 pm
Which makes the confirmation of intermediate species and structures between fish and land vertebrates all the more amazing.
Vázquez, et al., Modeling of Protein Interaction Networks, Complexus 2002: The model reproduces with noticeable accuracy the topological properties of the real PIN of the yeast S. cerevisiae.
This is not to say that such models accurately reproduce every aspect of biological evolution, but they do provide important insights.
Comment by Zachriel — September 2, 2008 @ 2:26 pm
September 2nd, 2008 at 2:39 pm
Zachriel:
And underscores how such examples radically change traditional thinking on the subject.
Zachriel:
Not sure why you referenced this paper again. I fully agree that "models" do not " accurately reproduce every aspect of biological evolution, but they do provide important insights."
Comment by Guts — September 2, 2008 @ 2:39 pm
September 2nd, 2008 at 3:25 pm
Honestly, Guts. I still don't see the distinction. Darwin predicted that fish and land vertebrates share a common ancestry and that the structures found in land vertebrates would have formed by gradual evolution of ancient structures in that common ancestor, and that those structures evolved from even more ancient structures. Darwin was reasonably close to the mark.
The insight is how genes can be strongly conserved, but the function still become highly modified—without intervention.
I took issue with your statement, and I still don't think you've been able to support it. What surprise there is comes from how deep the evolutionary relationships are, not that they exist. It's a matter of degree. Surprise is normal on the edges of science, or it wouldn't be so much fun. Evolutionary theory doesn't predict that new traits will suddenly appear. It predicts incremental adaptation of existing traits. That means the wings of birds are highly derived fins. And that humans are 'just' elaborated Deuterostomes.
Comment by Zachriel — September 2, 2008 @ 3:25 pm
September 2nd, 2008 at 3:49 pm
Zachriel:
In fact, during Darwin's time, the link between fins and limbs seemed impossible. It wasn't until 1988 that the link , surprisingly, was beginning to be established. The big surprise was that many of the components were already present. Thats the distinction, Darwin, or anyone after him, never fathomed that the genes necessary to build a multicellular body plan already existed in single celled organisms.
Zachriel:
Why did you add "without intervention"? That has no bearing on the FLE hypothesis whatsoever. The important part here, which once again supports FLE, is that "founder or seed" nodes from which new nodes arise are indeed most important. Indeed, the older nodes are also frequently evolutionary conserved across species and removal may result in disruption of a system.
Zachriel:
Zachriel, take a look at one of your latest responses:
It was just a one sentence assumption, you didn't even try to back it up. Whereas I gave multiple quotes and numerous examples (even your own!).
Zachriel:
Thats what I say here:
"The distinction is that the structures from which fins draw from are , much, much older, older than anyone expected."
Zachriel:
Even de-novo evolution of components evolve from existing structures, no one is claiming that evolutionary theory actualy predicts things will suddenly appear, that is ridiculous. Here is what standard evolutionary theory lead King, for example, to expect:
If you are working with the wrong framework, you're gonna have lots of "fun"
Comment by Guts — September 2, 2008 @ 3:49 pm
September 2nd, 2008 at 4:27 pm
Hi Richcheese
1) Yes, I had read the paper. I provided excerpts and included a link. Did you even bother to check THIS LINK? If you had, you would have noticed it was the full text, not just an abstract. It was from PubMed Central/Plos One.
2) The term "nearly absolute conservation" came from the body of the paper's text (not the abstract). I find it interesting that you can decide for me what I am focusing on. Nice trick.
3) Thank you for answering my question. However, I wasn't asking if you inferred design, I was asking if it surprised you. From your attitude, I am not surprised that you aren't surprised.
4) I would like to think I understand the difference between nerves and neurons. Do you think you can intimidate me with your superior knowledge? Good luck with that.
5) I grant you that assuming purpose is metaphysical. This is a Blog, not a peer-review of a formal paper. My ID hypothesis is that quantum effects are interconnect in 4D space-time. This would be a mechanism for things that appear to have reverse causation which can sound like asserting purpose.
I hope this has helped explain some things from my point of view for you.
Comment by Thought Provoker — September 2, 2008 @ 4:27 pm
September 2nd, 2008 at 4:31 pm
And yet Darwin's Theory of Evolution predicts this transition occurred based on the entire body of evidence in support of his theory. Handwaving aside.
Yes, some components were already present, including certain genes, as well as vertebrae, neck, lobed-fins, etc.
As Darwin didn't have a theory of genetics, that's not surprising. In any case, only some genes, but not all genes, exist in single-celled organisms. And we can expect whatever genetic structures led to early metazoa had ancestors.
The aforementioned properties require no foresight or intervention. They can occur naturally.
As I said, it doesn't take "front-loading" for an evolving system to exhibit those properties. "Front-loading" is an extraneous assumption.
It was a statement about what evolutionary theory would predict. Are you disclaiming this statement, or that the prediction is incorrect?
I probably would not have argued with that statement, and it is consistent with evolutionary theory. But the statement I did argue with was "standard evolutionary theory expects innovation, whereas the front-loading hypothesis expects 'deep borrowing.'" You drew a false comparison.
This is what King et al. say,
So the question is whether these molecules originated with the divergence of fungi or the divergence of metazoa themselves. It's