Blind cavefish can develop sighted offspring
by nullasalusWithin one generation, no less. From this 2008 article:
It's a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.
The ability was discovered when researchers mated fish from distinct populations that had been isolated in separate caves.
In some cases the first-generation offspring of such unions could see.
Anyway, some thoughts below the cut.
The article treats the ability of cavefish to produce sighted offspring given some particular conditions as exactly that: An ability. Something we should consider cavefish as being capable of. Fair enough, I say.
The first thing I'm wondering is, how should we regard this ability? I think it's a stretch to speak of (techne may jump on my usage of NS here) these cavefish 'being selected for their ability to produce sighted offspring in a single generation' – yet here they are. It seems more natural to chalk the ability up to a consequence of the underlying genetic operations, really: Distinct populations of cavefish differed in "how" they lost their sight, so when they were brought back together it was easier to "fill in the blanks".
The article mentions that "The genetic deficiencies from each parent's lineage were easily overcome by the strengths of the other." What deficiencies? They live in the dark. Cavefish need sight as much as they need bicycles, apparently – or at least this was the case for a long time. Granted, the writer simply knows that we normally don't think of blindness as expendable and is considering cavefish in that context.
But that leads to another question: Are eyes, even sightless eyes, "junk" for cavefish? It's context-dependent. It's not difficult to imagine a change in environment where sight actually becomes useful for cavefish, and not much more difficult to imagine two distinct populations ending up in that same (changed) environment. (The article doesn't mention whether these cavefish will interbreed on their own, or if they have to force them, I'll note.)
I'm not driving home some earth-shattering point here, but I leave readers with this suggestion: Just for fun, consider the ability of these cavefish from a design perspective. If you were assured that these cavefish were designs, how would you regard what's been revealed in this article? What would it say to you about selection, about variation, about species?
February 27th, 2011 at 9:56 am
a great experiment would be to genetically “knock out” the sightless eyes of blind cavefish and see if they are under positive selection pressure. If they are not this would be another case like this one and would be amazing evidence for the feasibility of frontloading
Comment by fifth monarchy man — February 27, 2011 @ 9:56 am
February 27th, 2011 at 1:25 pm
This reflects a loss that occurred secondarily in the lineage leading from the ancestor to the studied genome. This phenomenon (i.e. the secondarily loss of older genes) is not rare in evolution, the set of genes encoded by genomes may strongly change according to the lifestyle of the organisms.
Comment by Guts — February 27, 2011 @ 1:25 pm
February 27th, 2011 at 6:26 pm
This is suggestive of each separate population having pieces of the missing puzzle. Each population lost one part that impeded sight, but the merging of the populations enable genetic exchange, and of course you'll get sight. No big surprise.
This is like you and me each with andincomplete copy of the Bible. I realize I have one chapter missing in Mark, and you have one missing in Leviticus. We can exchange information and repair each other's books and then each have functional copies of the Bible. And that is exactly much of how the modern Bible is re-assembled from the ancient texts.
This information exchange if vital to slowing down genetic deterioration in populations and Joe Felsenstein argues that's why Muller's Ratchet is less in play with sexually reproducing populations. I illustrated Muller's Ratchet/Nachman's Paradox in asexual (technically speaking haploid) populations here: Nachman Purifying Selection. The cave fish are an illustration of how Muller's Ratchet is somewhat alleviated by allowing genetic exchange.
That's all that might be going on here with the fish. The had defective eyes, but each population had different sets of information causing the eye failure.
If this were not the case, then each of the separate populations would have had sighted offspring by now!!!!
The take home:
1. the observation does not affirm the power of selection
2. it shows that selection doesn't work to arrest decay of eyesight, if it did, the crossing of populations wouldn't have been needed in the first place to effect the change. They would have still been seeing.
Now if they didn't need to cross populations to create sight, it suggests that the eyesight is environmentally stimulated in the pheonotype. We call that developmental plasticity. One example is that grasshoppers change into the locust phenotype even if there was not a change in the genes, it was front loaded plascticity.
The bottom line, this example is not at all favorable to Darwinian evolution and blindness in organisms has been used by Allen Orr to criticize Daniel Dennett on Dennett's view that selection necessarily leads to design. To paraphrase Orr, seleciton can destroy design as much as build it. He used the example of a blind cavefish or crustacean to illustrate his point — specifically gammarus minus.
Comment by Salvador T. Cordova — February 27, 2011 @ 6:26 pm
February 27th, 2011 at 6:48 pm
Sure, that seems to be exactly what's going on. What I found interesting was this was framed as an ability on the part of the cave fish – and I think 'an ability to make (at least somewhat?) functional in 1 generation what has been broken for many, many generations' leads to some interesting questions about evolution both in a general sense, and from a design point of view. After all, "how" you lose information is a design consideration as well.
Comment by nullasalus — February 27, 2011 @ 6:48 pm
February 27th, 2011 at 7:46 pm
What I don't understand is why anyone would expend time on the subject when Muddy is waiting:
Comment by kornbelt888 — February 27, 2011 @ 7:46 pm
February 27th, 2011 at 7:47 pm
What I find interesting – from a design perspective – is that the rest of the genetic information for the "useless" eyes was intact enough that when the few "missing chapters" were inserted, the eyes came back to fully functioning form.
This after millions of years of dissuse – with no selective pressure acting to keep "junk" eye DNA intact.
Sounds like a pretty robust design to me.
Comment by Daniel Smith — February 27, 2011 @ 7:47 pm
February 27th, 2011 at 7:51 pm
To elaborate:
How does the genome "know" where to put the missing DNA (unless designed to do so)? Why would it yield a fully functioning eye on the first try (unless designed to do so)? Why didn't we get endless generations of trial and error?
Comment by Daniel Smith — February 27, 2011 @ 7:51 pm
February 27th, 2011 at 8:07 pm
Random mixing will suffice if we're dealing with small pieces of missing info. Consider the analogy of dark haired, somewhat dark skinned parents giving birth to a few light haired/light skinned offspring.
In like manner two blind fish could give birth to some seeing fish through random mixing if the genetic damage isn't too severe.
Null,
As I pointed out at UD, the fact the cave fish go blind is a powereful example of how selection DESTROYS design. In a dark environment, the ability to see causes more energy and nutrition to be consumed, so the blind are favored by selection! This is not a good thing. It actually shows selection does not have foresight, an important element of certain designs where short term sacrifice might be important for long term gains.
See: Dennett's Strange Idea for Recognizing Biological Function.
And I emphasize, "selection" is a horrible criteria for judging utility. By that standards, rapists and murderers are favorable individuals in the struggle for existence, as well as people who may be diseased (like sickle cell anemics or people with cystic fibrosis). My essay addressed why selection muddies and perverts straightforward perceptions in the engineering sense. I address the strange way blindness in cavefish is regarded as "good" by natural selection. I argue using selection as a means of measuring function will inhibit scientific understanding and lead to reciting meaningless tautologies.
Comment by Salvador T. Cordova — February 27, 2011 @ 8:07 pm
February 28th, 2011 at 5:24 pm
The term that describes this phenomenon is "genetic complementation." It's an extension of basic Mendelian genetics. In the simplest scenario, each population would be homozgous for a single mutation, and one would expect 100% of F1 hybrids to have normal vision.
In fact, between 1% and 40% of F1 hybrids had normal vison, depending on the particular populations crossed. That result indicates that there are several mutant genes in each population, so a smaller number of hybrids have the correct genetic combination to rescue the phenotype. The data is consistent with earlier research by the same group showing that the phenotype of these blind fish is influenced by mutant alleles at approximately 12 genes that control lens and eye development. Mutations at three or four of the 12 loci are sufficient to eliminate eye function. The percentage of F1s with normal vision will depend on the degree to which the two populations carry the same or different mutations: more closely related populations will have fewer F1 hybrids that can see.
Comment by Nick — February 28, 2011 @ 5:24 pm
March 1st, 2011 at 3:54 pm
As Nick said that was the key "ingredient". As Dr Behe noted there are many different ways to break things making it easier for darwinian mechanisms to oblige.
It is like taking two broken PCs- broken in different ways- and making one useful PC out of the two.
Comment by ID guy — March 1, 2011 @ 3:54 pm
March 1st, 2011 at 7:40 pm
what amazes me is that the fish carried the broken PCs around for so long for no apperent reason.
peace
Comment by fifth monarchy man — March 1, 2011 @ 7:40 pm
March 1st, 2011 at 9:54 pm
If it was an unnecessary part that was broken- why care about/ repair something you aren't using?
Comment by ID guy — March 1, 2011 @ 9:54 pm
March 2nd, 2011 at 8:20 am
I would not expect the fish to care about or fix the "junk" eyes.
I would expect them to pitch the dead weight and get on with their lives.
There is undoubtedly a cost involved to keep around an organ that is useless to you. Just as it costs my computer in overall efficiency to keep around corrupted files.
Not only do these fish keep the broken organs around but apparently they make sure that they don’t degrade further for no apparent reason .
I find that fascinating
Peace
Comment by fifth monarchy man — March 2, 2011 @ 8:20 am
March 2nd, 2011 at 8:35 am
This finding sits neatly within an orthodox evolutionary framework. Most important, going to the original paper, it is notable that this research was conducted to test a prediction arising out of that framework, as well as previous observations regarding the results of hybridization. That's how science is done.
Comment by Reciprocating Bill — March 2, 2011 @ 8:35 am
March 2nd, 2011 at 10:10 am
Hi nullasalus,
Yeah, this concept of "junk" is really silly. Personally, I think it would be better to cast these phenomena in terms of potentiality and actuality together with intrinsic finality/natural ends/natural inclinations or even intrinsic natural ends/inclination. And as stated before, natural selection is merely descriptive, not prescriptive so we need to focus on the causes of biological change to understand it.
For example, certain genomes just have the intrinsic natural inclination to produce eyes and sight. This potentiality is not always actualized just like the potentiality for water to turn into ice is not always actualized (it might be changed into hydrogen and oxygen before it ever had the chance to be actualized into ice or whatever).
The point being, while the eyes and the genes coding for the eyes might not be functionally relevant to the fitness of cave fish, whenever the genes are present, it still has the intrinsic natural inclination to produce eyes and even perhaps sight (as the above study suggests). This potentiality is not actualized by itself, but perhaps by environmental pressures which might cause epigenetic changes which in turn might actualize the potentiality of the genes coding for the eyes and sight. An in depth study of the epigenetic changes would be fascinating as I am pretty sure it played a role.
To answer your question:
From a teleological perspective this study just again confirms the presence of intrinsic finality/natural ends/natural inclinations or intrinsic natural ends/inclinations in nature, this time specifically related to the intrinsic finality of genomes naturally inclined to produce eyes and sight. While they have the potential to produce eyes and sight, this might not be always actualized, but sometimes when it is, it might be functionally relevant to the fitness of the organism.
Comment by Techne — March 2, 2011 @ 10:10 am
March 2nd, 2011 at 11:10 am
fifth monarchy man,
A few points (if I may)-
1- We don't know if the fish can "ditch them" altogether. Also perhaps that cost isn't so much that it cannot be overcome.
2- Think of them as peripheral devices- for example if you have a corrupted path for your printer it won't affect your computer's performance if you never use your printer. So the proper example would be two computers that have but never use their peripheral devices, that the two have damage to the same device, and that the damage is different- one has a corrupted file path and the other hs some bad hardware on the printer board.
Comment by ID guy — March 2, 2011 @ 11:10 am
March 2nd, 2011 at 11:15 am
Good day to you, sir. What orthodox evolutionary framework would that be? This finding fits neatly within baraminology, which is an evolutionary framework. It also fits in neatly with front loaded evolution. So could you please clarify what you are saying?
Also there isn't anything in the theory of evolution that states take two isoate populations, have random effects cause different damage to the same body part, mate the two populations and have that once damaged body part rgain its original functin.
So please, sir, explain yor comment.
Comment by ID guy — March 2, 2011 @ 11:15 am
March 2nd, 2011 at 11:18 am
The next step is to take these hybrids ith sight, place them into a lightless cave- and see how longs it takes to get 100% blind fish. Then see if there are any new changes that caused the damage.
Comment by ID guy — March 2, 2011 @ 11:18 am
March 2nd, 2011 at 11:21 am
Reciprocating Bill wrote:
Orthodox? That’s a term usually used in a religious context.
So what does that make people who question the orthodoxy? Heretics?
Notice how Bill doesn’t make an argument here, just a vague appeal to authority.
Comment by JOHN_A_DESIGNER — March 2, 2011 @ 11:21 am
March 2nd, 2011 at 1:35 pm
It's also a synonym for "conventional" and "well-established".
Comment by KC — March 2, 2011 @ 1:35 pm
March 2nd, 2011 at 2:37 pm
That makes no difference. Bill is making an appeal to authority and the "orthodox interpretation" much the way religious people defend their orthodoxy. Science on the other hand needs to be tentative which means it must be open to skepticism and criticism. Indeed a Popperian falsificationist approach is intrinsically a critical approach. That should be the approach with evolutionary science. Unfortunately, some people cannot defend their position without making quasi-religious or pseudo-religious appeals to some kind of vaguely defined orthodoxy.
Comment by JOHN_A_DESIGNER — March 2, 2011 @ 2:37 pm
March 2nd, 2011 at 2:50 pm
So according to Reciprocating Bill, this finding sits neatly within the framework of "not knowing" and "differing theories".
Where have I heard that before? Oh yeah!
Comment by chunkdz — March 2, 2011 @ 2:50 pm
March 2nd, 2011 at 3:22 pm
So you disagree with him when he wrote:
.
Comment by KC — March 2, 2011 @ 3:22 pm
March 2nd, 2011 at 3:35 pm
What "orthodox framework" are you guys referring to? The "orthodox framework" that has embraced Dollo's Law of Irreversability for the last hundred years or so – only to have studies like this one shatter the orthodoxy?
Sorry, but this prediction arose from a CHALLENGE to orthodoxy, not adherence to it.
When "orthodox framework" simply means "I'm right no matter what happens" then it isn't very useful.
Comment by chunkdz — March 2, 2011 @ 3:35 pm
March 2nd, 2011 at 4:25 pm
I don’t think Dollo’s “Law” applies here. If we were looking only at one lineage in one cave, then yes, it would be highly improbable that restoration of sight would occur, for precisely the reasons Dollo laid out. But that isn’t what we are talking about. Instead, we are looking at several independent, isolated populations, which evolutionary theory predicts are likely to have acquired different patterns of mutations that resulted in loss of vision (there are 12 unlinked eye loci involved). Impairment of vision via mutation to these loci can happen different ways. Given the random nature of mutation occurrence, the authors reasoned that if they crossed fish from different independent lineages, then they might genetically complement each other and vision might be restored in some of the F1 hybrids. This is hardly a ‘shattering’ of orthodoxy. Instead, it’s the authors using orthodox, mainstream evolutionary theory to predict an outcome, and being right.
Comment by KC — March 2, 2011 @ 4:25 pm
March 2nd, 2011 at 4:29 pm
So this does fit in neatly with both baraminology and FLE!
The theory of evolution doesn't make such a prediction. Convergent evolution- either way (destruction nor construction) is a prediction of the theory of evolution.
Comment by ID guy — March 2, 2011 @ 4:29 pm
March 2nd, 2011 at 4:41 pm
The theory of evolution doesn't make such a prediction. Convergent evolution- either way (destruction nor construction) is a NOT prediction of the theory of evolution.
The theory doesn't predict sexual reproduction and it doesn't predict gametes will have half of the chromosomes that somatic cells have.
Comment by ID guy — March 2, 2011 @ 4:41 pm
March 2nd, 2011 at 4:42 pm
Evolutionary theory predicts genetic divergence via reproductive isolation. That's what we are talking about here, not convergent evolution.
Comment by KC — March 2, 2011 @ 4:42 pm
March 2nd, 2011 at 4:46 pm
The article is about convergent evolution – mutations reaching the same (end-point), albeit different, "solution" in indepedent populations.
The theory doesn't predict that. And thereby doesn't predict the mating of two independent populations will restore the loss.
Comment by ID guy — March 2, 2011 @ 4:46 pm
March 2nd, 2011 at 4:49 pm
Baraminology and FLE predict genetic divergence via reproductive isolation.
Comment by ID guy — March 2, 2011 @ 4:49 pm
March 2nd, 2011 at 4:52 pm
One of the referenced papers from the article:
Comment by ID guy — March 2, 2011 @ 4:52 pm
March 2nd, 2011 at 5:30 pm
So what?
Comment by KC — March 2, 2011 @ 5:30 pm
March 2nd, 2011 at 5:33 pm
Too bad what we are talking about (and what the study was about) is restored vision through complementation.
Comment by KC — March 2, 2011 @ 5:33 pm
March 2nd, 2011 at 5:42 pm
Baraminology and FLE predict genetic divergence via reproductive isolation.
So the "orthodox evolutionary framework" is unnecessary.
Due to convergent evolution.
Comment by ID guy — March 2, 2011 @ 5:42 pm
March 2nd, 2011 at 5:43 pm
The article is about convergent evolution – mutations reaching the same (end-point), albeit different, "solution" in indepedent populations.
The theory doesn't predict that. And thereby doesn't predict the mating of two independent populations will restore the loss.
Comment by ID guy — March 2, 2011 @ 5:43 pm
March 2nd, 2011 at 6:13 pm
KC:
Does Dollo's Law have an exclusion for interbreeding populations? Don't think so.
(Sorry, but if losing eyesight for a million years and then regaining the same complex function is not a violation of Dollo's Law then I don't know what else could be.)
You unwittingly emphasize my point. Dollo's Law WAS orthodoxy – until it fell into disrepute. Orthodoxy is Orthodox – unless it's not.
unless it's not
unless it's not
unless it's not
Here's an abstract from one of the above citations.
Sounds like a challenge to the orthodoxy of Dollo's Law to me.
Comment by chunkdz — March 2, 2011 @ 6:13 pm
March 2nd, 2011 at 6:23 pm
From what chunkdz posted it looks like Dollo's Law doesn't apply, which of course, was chunkdz's point.
Comment by ID guy — March 2, 2011 @ 6:23 pm
March 2nd, 2011 at 8:07 pm
I agree that there is hybridization going on here, but where is the prediction from orthodox evolutionary theory that a complex function like sightedness could not only be lost but preserved for a million years and then reactivated? That is a prediction you would expect from a design friendly "front loaded" view of evolution. Of course, neither view really explains the origin of eyes or sightedness in the first place.
Comment by JOHN_A_DESIGNER — March 2, 2011 @ 8:07 pm
March 2nd, 2011 at 8:34 pm
… anything and everything.
Comment by Daniel Smith — March 2, 2011 @ 8:34 pm
March 2nd, 2011 at 8:48 pm
ID Guy:
I doubt clarification among these and similar alternatives is really required. But in the event that it is, I am saying that the research reported in this article was motivated by the components of mainstream evolutionary theory that were of concern to the authors, yielding findings consistent with predictions they made from within that framework.
John_A_Designer:
"Orthodox" may also denote something of the ordinary or usual type, and that is the sense in which I intended it. In this instance I refer to mainstream evolutionary biology as distinct from, for example, design theory. I should have thought that obvious in this context. But perhaps not.
I simply intended that the research was motivated by predictions that arose within the context of mainstream evolutionary theory, and that the findings comport with those predictions. That framework was not supported by appeal to authority or "orthodoxy" in the sense in which you deployed that term above, but rather by the empirical findings.
As I said earlier, "Most important, going to the original paper, it is notable that this research was conducted to test a prediction arising out of that framework, as well as previous observations regarding the results of hybridization."
Comment by Reciprocating Bill — March 2, 2011 @ 8:48 pm
March 2nd, 2011 at 8:49 pm
Except, apparently, a precambrian rabbit…
Comment by ID guy — March 2, 2011 @ 8:49 pm
March 2nd, 2011 at 8:52 pm
Except, apparently a precambrian rabbit.
Comment by ID guy — March 2, 2011 @ 8:52 pm
March 2nd, 2011 at 9:04 pm
Excuse me but as we have been discussing the predictions had nothing to do with that framework. And there are only two vague references to "evolution" in the paper.
and
So you can repeat your claim as many times as you like but that ain't going to change the fact that it is flat out wrong.
Comment by ID guy — March 2, 2011 @ 9:04 pm
March 2nd, 2011 at 9:30 pm
He also is trying to paint Dollo's "Law" as strict orthodoxy. It's not, and hasn't been since at LEAST the Modern Synthesis (see pp. 428-430 of Dobzhansky's Genetics of the Evolutionary Process. In fact, for such a big bad orthodoxy, the paper we are discussing now doesn't mention it. Not even once.
Comment by KC — March 2, 2011 @ 9:30 pm
March 2nd, 2011 at 9:44 pm
The point was that Dollo's law was strict orthodoxy- meaning at one time, but not now. That would be the reason it isn't mentioned in the paper.
The word "orthodox" has little meaning- might as well just say contemporary, and leave it at that.
Comment by ID guy — March 2, 2011 @ 9:44 pm
March 2nd, 2011 at 9:57 pm
JAD writes:
I suggest Dobzhansky;s Genetics of the Evolutionary Process for starters, written 41 years ago. It gives one the tools to enable understanding why we might expect such things to happen. It also gives one a sense of what kinds of boundary conditions there are on it. Essentially, the probability of reversibility fades not so much as time increases, but with the number of successive substitutions that have occurred in the interval.
Comment by KC — March 2, 2011 @ 9:57 pm
March 2nd, 2011 at 9:58 pm
Another storm in a bullshit teacup.
Comment by KC — March 2, 2011 @ 9:58 pm
March 2nd, 2011 at 10:04 pm
Reciprocating Bill:
One more time for the hard of hearing, …
Your "ordinary" or "usual" orthodoxy can't even make up it's mind what is driving evolution.
There is no "orthodox evolutionary framework" to work from. There isn't an "ordinary" or "usual" evolutionary framework. It doesn't exist. It's a fairytale.
If anything, this research team has challenged a century old orthodoxy built upon some very fallacious assumptions.
Comment by chunkdz — March 2, 2011 @ 10:04 pm
March 2nd, 2011 at 10:38 pm
Actually I said that the so-called orthodoxy (that Reciprocating Bill was referring to) included Dollo's Law. I don't think I'm alone in that assertion.
Cruikshank and Paterson wrote in 2006:
Colin and Cipriani in 2003:
Collin and Miglietta in 2008:
Curland, Canback, and Berg, 2007:
Igic, Bohs, John, 2006:
And so on…
There is no real orthodoxy, though it is useful for culture warriors to pretend that there is.
Comment by chunkdz — March 2, 2011 @ 10:38 pm
March 2nd, 2011 at 10:46 pm
Comment by KC — March 2, 2011 @ 10:46 pm
March 2nd, 2011 at 10:51 pm
An assertion is incorrect, regardless.
Comment by KC — March 2, 2011 @ 10:51 pm
March 2nd, 2011 at 10:59 pm
From the body of the paper, not just the abstract:
Doesn't sound like they agree with you there.
Comment by KC — March 2, 2011 @ 10:59 pm
March 2nd, 2011 at 11:13 pm
Sounds like they don't agree with Dollo's Law. Nor do any of the other research papers I quoted. They do however acknowledge that Dollo's Law has been the "dominant paradigm" until very recently.
Wow, it's almost as if…there isn't an orthodox evolutionary framework!
Comment by chunkdz — March 2, 2011 @ 11:13 pm
March 3rd, 2011 at 12:47 am
So let me try to get this straight, Dollo's Law is no longer an orthodox part of the theory of evolution, though it once was, but Dobzhansky and the neo-Darwinian synthesis still is? Who decides when something that is or was orthodox becomes unorthodox? Or is it just a kind of hold-your-finger-to-the-wind consensus kind of thing?
What pages are you talking about?
Comment by JOHN_A_DESIGNER — March 3, 2011 @ 12:47 am
March 3rd, 2011 at 1:14 am
Dollo's law is off point, x2.
First, it is inapplicable to this phenomenon, despite superficial appearance of relevance, as noted by KC. The genetic re-expression of a lost adaptation accomplished by means of complementation =/= the re-evolution "from scratch" of that adaptation in the sense Dollo intended.
Second and more generally, it doesn't follow from the fact that particular hypotheses within evolutionary biology suffer reversals that the overarching framework has ceased to be productive. To the contrary: reversals of theoretical fortune are a hallmark of a living empirical science in which theory and the empirical research that arises from that theory are in dialog.
Like it or not, this paper describes research that addresses a prediction that flows from a particular theoretical model of the loss of adaptations that is situated squarely within mainstream evolutionary biology (particularly relative to empirically unproductive fringe hypotheses such as design theory and baraminology), and and describes results that comport comfortably with that prediction.
Advocates of ID would do well to emulate that process.
Comment by Reciprocating Bill — March 3, 2011 @ 1:14 am
March 3rd, 2011 at 7:48 am
Hi John,
When Dollo proposed his "Law", back in the 19th century he based it mainly on paleontological data, and his version was absolute– irreversibility was not possible. Mendel's work had not even been discovered, then, of course. The Modern Synthesis changed that view, especially because it showed, in the light of genetics, how evolution is a property of populations, a statistical phenomenon. Simpson restated Dollo's "Law" as a probability argument. In Dobzhansky's book (pp. 428-430), the principle is essentially stated this way: the more mutations involved, the less likely the reversibility– its not absolute. This, I would argue, is the mainstream view. It's certainly the one I was taught. As such, the results from the paper we have been discussing are not a 'shattering of orthodoxy'. Well, maybe before Mendel ;0 I recommend the whole book because the basic principles in it are still sound– some has had to be revised as new data and techniques have emerged, of course, but in general the book still provides a sound look at evolutionary theory from a genetic perspective. Much of what the architects of the Modern Synthesis proposed remains valid, and I recommend reading books and papers by Fisher, Simpson, Stebbins, Wright and Dobzhansky for that reason. I also recommend keeping up with the literature as it emerges, because some things have changed, and will change. As Reciprocating Bill nicely stated:
Comment by KC — March 3, 2011 @ 7:48 am
March 3rd, 2011 at 8:23 am
KC
Hey that's the book where Dobzhansky described natural selection as a composer/editor or sculptor or whatever. One of the many key components of the modern synthesis that is crumbling.
Comment by Guts — March 3, 2011 @ 8:23 am
March 3rd, 2011 at 8:25 am
That is your favorite drink. Too bad you have to spray the people around you with it.
Comment by ID guy — March 3, 2011 @ 8:25 am
March 3rd, 2011 at 8:30 am
You want ID to emultae your lies and bullshit? That is all you are doing with your posts (in this thread).
Is that what it takes to become science? Just spew lies and bullshit and your position is all set.
The take home message from all this is "mainstream/ orthodox" evolutionary theory is indistinguishable from baraminology and FLE.
Thanks to KC and Reciprocating Bill for making that very clear.
Comment by ID guy — March 3, 2011 @ 8:30 am
March 3rd, 2011 at 11:07 am
Consider this, besides several species of fish many other kinds of animals (worms, crayfish, salamanders and a variety of insects etc.) found living in caves adapt to their environments in remarkably similar ways: loss of eye sight/eyes, loss of pigmentation and enhancement of other senses. What best explains this convergent kind of adaptation? Natural selection acting on random mutation that just coincidently ends up with all the same adaptations? Or is this a genuine case pre-adaptation? Consider what this pre-adaptation hypothesis implies. Since, these kind of adaptations are shared by several distinct phyla it appears that they must have evolved before any of these phyla existed. This is something that we would expect from an unorthodox view like front loaded evolution.
Comment by JOHN_A_DESIGNER — March 3, 2011 @ 11:07 am
March 3rd, 2011 at 12:31 pm
John,
I think one question we should be asking is, are sight and pigmentation loss actually adaptations? That is, does being blind or lacking pigment significantly increase the fitness of these individuals in the cave environment?
Comment by KC — March 3, 2011 @ 12:31 pm
March 3rd, 2011 at 12:43 pm
Reciprocating Bill:
Lol! A Law of evolution is inapplicable to…evolution?
It's not "off point", Bill, it's wrong. Wrong because it was based upon a flawed view of evolution as some kind of linear one way trip. When we learned that metazoans can transfer chunks of DNA horizontally we don't say Darwin was "off point", we say he was wrong. There's no shame in that unless you're some kind of weird Darwin or Dollo sycophant.
Hmmm. Good thing I never said that then.
Nope. The prediction came from the framework of Genetics, not Evolutionary Biology. As has been pointed out to you twice now, there is no agreement on what drives the evolution of cave-blindness. Your "orthodox framework" is missing a few struts. But we don't need to know anything about the evolution of blindness to make this prediction. We just need simple Mendelian Genetics.
Once again, this shows that what you refer to as "orthodox evolutionary framework" is really just the stenographer and historian for the real biological sciences. Keep your eraser handy, stenographer. You'll need it.
Comment by chunkdz — March 3, 2011 @ 12:43 pm
March 3rd, 2011 at 1:05 pm
That would explain the 100% of the population is blind part. That is how it is done, right? Take a look at the output and then make something up, for example the reason why the whole population is blind is because the blind fish in a lightless cave were better adapted to their environment and over the course of X generations, being better adapted they out-reproduced their sighted counterparts such that blind fish took over completely.
Say that with a nice silky-smooth voice and you have the tellings of orthodox evolutionary theory.
Comment by ID guy — March 3, 2011 @ 1:05 pm
March 3rd, 2011 at 1:11 pm
Not necessarily.
Comment by KC — March 3, 2011 @ 1:11 pm
March 3rd, 2011 at 1:13 pm
Yes it would if done in a silky-smooth voice using the words I provided.
Comment by ID guy — March 3, 2011 @ 1:13 pm
March 3rd, 2011 at 1:14 pm
That and the jedi hand-wave.
Comment by ID guy — March 3, 2011 @ 1:14 pm
March 3rd, 2011 at 1:54 pm
Another question that might be good to ask is, what ecological characteristics do caves have in common besides darkness?
Comment by KC — March 3, 2011 @ 1:54 pm
March 3rd, 2011 at 2:18 pm
Wetness?
Comment by chunkdz — March 3, 2011 @ 2:18 pm
March 3rd, 2011 at 2:27 pm
Yes, that way we would have more juicy stuff to throw into the story.
1- Water- the fish need water and oxygen
2- Got to have some food- so a food source that they can get to without having to see it
3- Predation- perhaps a lack of predators
4- Maybe some real scary features that led to the demise of the sighted fish
So is James Earl Jones available? Should someone work on that while we hash out the narration?
I think this is going rather well.
Comment by ID guy — March 3, 2011 @ 2:27 pm
March 3rd, 2011 at 2:45 pm
That's one. Yep.
Comment by KC — March 3, 2011 @ 2:45 pm
March 3rd, 2011 at 2:47 pm
Any others?
Comment by KC — March 3, 2011 @ 2:47 pm
March 3rd, 2011 at 2:53 pm
Darkness?
Comment by Guts — March 3, 2011 @ 2:53 pm
March 3rd, 2011 at 2:56 pm
Huuked on fonix werked fer me
Comment by Guts — March 3, 2011 @ 2:56 pm
March 3rd, 2011 at 3:20 pm
I asked besides darkness. One that came to me was relatively constant temperature and humidity. But let's take another look at darkness. Can you think of any consequences darkness might have on the community of organisms?
Comment by KC — March 3, 2011 @ 3:20 pm
March 3rd, 2011 at 3:32 pm
Yeah I know I was just being a dunce. Sorry about that, just ignore me.
Comment by Guts — March 3, 2011 @ 3:32 pm
March 3rd, 2011 at 3:36 pm
At least you understood the question.
Comment by KC — March 3, 2011 @ 3:36 pm
March 3rd, 2011 at 3:36 pm
Cave fish will choose their mates based on personality?
Comment by chunkdz — March 3, 2011 @ 3:36 pm
March 3rd, 2011 at 3:39 pm
LOL.
Comment by KC — March 3, 2011 @ 3:39 pm
March 3rd, 2011 at 3:41 pm
Well one straightforward thing about darkness is that they are essentially blind anyway, so they rely more and more on other senses, and thus if mutations occur that affect sight, it doesn't get weeded out. Thats just my shoot from the hip wildly ignorant guess though.
Comment by Guts — March 3, 2011 @ 3:41 pm
March 3rd, 2011 at 3:48 pm
That's a good relevant point. But when I said community of organisms, I was thinking of all the species in the cave, and not just animals.
Comment by KC — March 3, 2011 @ 3:48 pm
March 3rd, 2011 at 4:02 pm
No photosynthesis. Therefore, no herbivores. Cave dwelling animals will eat other cave dwelling animals, fungus/bacteria, or detritus washed in to the cave.
(That goes a long way to explaining the lack of herbivores among wandering monsters in Dungeons and Dragons campaigns).
Comment by Nick — March 3, 2011 @ 4:02 pm
March 3rd, 2011 at 4:25 pm
So, not only are caves dark, they are relatively nutrient poor. What kind of traits would we expect to thrive in that kind of an environment? For example, what if a sighted fish from the surface of the same species gets washed into the cave after a flash-flood? What traits might it possess (besides depending on sight) that would make it difficult to survive in a cave?
Comment by KC — March 3, 2011 @ 4:25 pm
March 3rd, 2011 at 5:22 pm
This must be how Rudyard Kipling wrote those charming children's stories…
Comment by chunkdz — March 3, 2011 @ 5:22 pm
March 3rd, 2011 at 5:25 pm
Here is something interesting:
More recent research by Jeffery indeed confirms that the same up-regulated sonic hedgehog gene (shh) that is the cause of the loss of the eye in the Astyanax mexicanus is also the cause of a larger jaw, an increase in the number of teeth and taste buds etc.– apparently useful adaptations for a fish inside a dark cave environment. So the loss of the eye, which isn’t needed any how, is apparently all just coincidence. After all, how would a mindless, purposeless natural evolutionary process lacking any kind of foresight know something like that?
I wonder if the same shh gene plays a similar role in other cave animals.
Comment by JOHN_A_DESIGNER — March 3, 2011 @ 5:25 pm
March 3rd, 2011 at 6:06 pm
You can make fun of my questions all you like, but they have a purpose: to try and help us get a sense of the kinds of complexities involved when trying to tease out the natural history of these organisms. Some of the things may be relatd in unexpected ways (as John's last post suggests), while some may actually be independent.
Comment by KC — March 3, 2011 @ 6:06 pm
March 3rd, 2011 at 7:43 pm
On the other hand…
So it appears that loss of eye sight/eyes may be an adaptation after all. At least according to this Harvard study.
Comment by JOHN_A_DESIGNER — March 3, 2011 @ 7:43 pm
March 3rd, 2011 at 8:35 pm
Man, you would expect a shh gene to be involved with vocalization.
Comment by ID guy — March 3, 2011 @ 8:35 pm
March 3rd, 2011 at 9:26 pm
Sure.
Atheist motto: "We don't know anything for sure – except that there is no God."
Atheism: Smug. Irrational. Nasty. – We've got it all!
Atheism: We hate that which doesn't exist.
Liberalism: Any scum-sucking dirtbag who disagrees with us is uncivil.
Liberalism: We are extremely tolerant of all views we agree with.
Tee Hee!
Comment by Daniel Smith — March 3, 2011 @ 9:26 pm
March 3rd, 2011 at 9:32 pm
KC:
We're ID'ers. We're not unfamiliar with the concept of 'complexity of natural history'. It's kind of 'our thing'.
Please continue – I was just having a little fun.
Comment by chunkdz — March 3, 2011 @ 9:32 pm
March 3rd, 2011 at 11:15 pm
Chunkdz,
Dollo's law is inapplicable to the recovery of functioning eyes in cave fish by means complementation.
Wrong level of abstraction. It is your citation of Dollo's law in this context that is off point, whether he was right or wrong. Specifically, your citation is off point because the the re-emergence of vision in these fish occurs in a manner that bears no relationship to the re-evolution of lost complex features Dollo surmised impossible.
Further, you cite the reversal of Dollo's fortunes to advance your peculiar claim that nothing that may be broadly characterized as a mainstream evolutionary conceptual framework exists – within which (I assert) this paper nicely nests. But, as I stated earlier, it doesn't follow from the fact that particular hypotheses within evolutionary biology suffer reversals that the overarching framework has ceased to be productive. To the contrary: reversals of theoretical fortune are a hallmark of a living empirical science in which theory and the empirical research that arises from that theory are in dialog.
That doesn't help you, because the authors' conceptualization of the genetics in question is inextricably wed to contemporary evolutionary theory, specifically (to cite one example) the fact that the similarities that remain among the now disabled genetic instructions for eye-building reflect the descent of these 29 populations from an eye-bearing common ancestor. The rationale for the prediction that motivated the study is similarly explicitly and inextricably intertwined with that evolutionary understanding of the relevant genetics, as is their conceptualization of their results.
Comment by Reciprocating Bill — March 3, 2011 @ 11:15 pm
March 4th, 2011 at 9:22 am
Dollo's Law is inapplicable, period- that was the whole point. And the theory of evolution did not predict recovery by means of complementation.
Right, you baldly asserted and have since been corrected. Yet you persist. Trying to have a discussion with you is like playing tennis with a blind person- no returns, just the same bad play over and over.
Wrong again. The genetics is inextricably linked to Gregor Mendel's work, which was stolen by evolutionists and then forced into their "theory".
If we use evolutionary "logic" I would say that Reciprocating Bill and Zachriel are one in the same, ie same insipid comments
Comment by ID guy — March 4, 2011 @ 9:22 am
March 4th, 2011 at 9:26 am
Blah, blah, blah. Reciprocating Bill baldly asserts, gets corrected, baldly assetrts, gets corrected and baldly asserts again. Insipidity at its finest.
Comment by ID guy — March 4, 2011 @ 9:26 am
March 4th, 2011 at 9:27 am
Mendelian genetics, and not the theory of evolution, is the framework for this experiment. and just because the theory of evolution stole Mendel's work and tried to pawn it off as its own just further exposes evolutionary desperation.
Comment by ID guy — March 4, 2011 @ 9:27 am
March 4th, 2011 at 11:49 am
By way of clarification here is what ID’ists, including me, typically think about the kind of evolution we see in cave animals:
What I find interesting is not micro evolutionary change of a single species (that indeed can be explained by neo-Darwinian theory) but the fact this same basic adaptation is used over and over again, not just by different species, but widely divergent different phyla. That clearly implies some kind of pre-adaptation which is unexplained by any kind of Darwinian/ neo-Darwinian mechanism.
Comment by JOHN_A_DESIGNER — March 4, 2011 @ 11:49 am
March 4th, 2011 at 2:30 pm
Reciprocating Bill:
Let me check what Dollo said again. Maybe I missed something.
Whoa! How did I miss that?!? I guess you're right, Bill!
That's sort of like saying that there's some Law that says humans can never fly, but that law doesn't apply to the Wright Brothers because they used a plane.
Usually when one speaks of a "framework" they are referring to something sturdy, fixed, and reliable – as in the framework of a skyscraper or the bulkheads of a ship.
If you'd like to re-characterize the term to mean some gelatinous blob that happens to lean whicheverway the wind is blowing then I'll just say have fun with that. Science will march on despite you.
Anyhow, we'd love to hear you tell us how Dollo's Law doesn't apply to limpets, parasites, mites, and sand boas.
Is it because Dollo's Law doesn't apply to anything which breaks Dollo's Law?
Comment by chunkdz — March 4, 2011 @ 2:30 pm
March 4th, 2011 at 2:41 pm
Huppop K (1987). Food-finding ability in cave fish (Astyanax fasciatus). Int. J. Speleol. 16: 59-66
From the Abstract:
Comment by KC — March 4, 2011 @ 2:41 pm
March 4th, 2011 at 3:12 pm
JAD:
Jeffery's work on the hedgehog gene which you cited would indicate otherwise. The Hedgehog gene family is involved in eye development of both vertebrates and invertebrates.
Comment by KC — March 4, 2011 @ 3:12 pm
March 4th, 2011 at 4:08 pm
No it implies that pre-adaptation occurred during the pre-Cambrian era. That strengthens the idea of some kind of front loading. In other words, what we are observing is not natural selection chancing on the same solution over and over again but rather there was a solution that was already genetically there for natural selection to choose. That of course raises the question of how and why “an unguided, unplanned process of random variation and natural selection" anticipated these kinds of solution hundreds of millions of years in advance.
Comment by JOHN_A_DESIGNER — March 4, 2011 @ 4:08 pm
March 4th, 2011 at 4:18 pm
I'm not talking about a preadaptation. I'm talking about degenerative mutations to the hedgehog genes which will have similar effects on eyes in numerous diverse taxa because they influnce similar developmental paths. There is nothing in that scenario that precludes Darwinian processes.
Comment by KC — March 4, 2011 @ 4:18 pm
March 4th, 2011 at 5:38 pm
I forgot. Darwinism explains everything, even those things we don’t understand.
Comment by JOHN_A_DESIGNER — March 4, 2011 @ 5:38 pm
March 4th, 2011 at 5:54 pm
You haven't thought through the genetic, phylogenetic, and ecological pieces to the situation. Thus you must resort to petulant, content-free sarcasm. Nice.
Comment by KC — March 4, 2011 @ 5:54 pm
March 4th, 2011 at 6:51 pm
Ironically even Darwin did not invoke Darwinism to explain eyeless cave animals.
Notice that the explanation for eye loss, "disuse", is essentially a Lamarkian one. Darwin may have not been right, but he certainly felt free to posit other explanations.
But today we have to dogmatically accept Darwinism as if it was some kind of sacrosanct religious creed. Why?
Comment by JOHN_A_DESIGNER — March 4, 2011 @ 6:51 pm
March 4th, 2011 at 7:05 pm
You are a beautiful man.
Comment by kornbelt888 — March 4, 2011 @ 7:05 pm
March 4th, 2011 at 7:20 pm
Comment by Guts — March 4, 2011 @ 7:20 pm
March 4th, 2011 at 8:24 pm
A defective simile, but one that can be rescued with a small change. Here it is:
"That's sort of like saying there's some Law that says humans can never fly by flapping their forelimbs, but that law doesn't apply to the Wright Brothers because they used a plane."
That works.
"Framework" is, of course, metaphorical, and what counts in grasping metaphor is attentiveness to the features that are relevant in a given context. Since "conceptual framework" has a history as metaphor, we needn't look far for those features, in this instance connectedness and structure – often (perhaps always) provisional – that scaffold the further acquisition of knowledge. Mainstream evolutionary biology has unquestionably provided a framework in this sense for decades.
Further, the key measure of the value and usefulness of a scientific framework is not it's rigidity, but rather its ability both to guide empirical research by providing testable entailments and to provide a context that renders the resulting observations meaningful. The authors of this study operated from within the framework of contemporary evolutionary theory, deriving thereby both their immediate research question and mapping thereby their results into a larger context.
Comment by Reciprocating Bill — March 4, 2011 @ 8:24 pm
March 4th, 2011 at 8:28 pm
IDGuy:
Hard to imagine a higher compliment. Alas, it isn't so.
Comment by Reciprocating Bill — March 4, 2011 @ 8:28 pm
March 4th, 2011 at 8:30 pm
What I see at work here is the inherent teleology of nature. Nature—everywhere you look—acts as if it is obeying a master plan.
Darwinian evolution can destroy eyesight, but when given the opportunity, the pieces of the puzzle snap back into place.
Comment by Daniel Smith — March 4, 2011 @ 8:30 pm
March 4th, 2011 at 8:55 pm
A framework which just happens to be indistinguishable from baraminology. The theory of evolution sure as heck didn't predict complementary genetics.
So the question is what guidance was the theory of evolution to this study? Baraminologists conducting the same study under their framework would produce the same results. They could even stumble onto it just by testing if the different populations were indeed different species or just variations within a Kind. That and plain ole Mendelian genetics are the only framework required for this sort of discovery.
But I am sure Reciprocating Bill will be back with another round of entertaining bald assertions and misguided attempts at trying to salvage a failed/ fruitless heuristic.
Comment by ID guy — March 4, 2011 @ 8:55 pm
March 4th, 2011 at 9:04 pm
Reciprocating Bill:
Yeah, I'd agree that Dollo's Law is about as useful as a Law that states that humans can't fly by flapping their forearms.
Problem is, even the most direct interpretation of Dollo's Law is apparently in question. Apparently evolution can flap it's forearms in ways which Darwinists never imagined.
It's not Dollo's fault. He had no idea how evolution works. But it is certainly funny listening to Darwinistas trying to make a probability argument about a certain kind of evolution being impossible while the IDiots present them with research papers proving them wrong.
If we proceeded under the framework of Dollo's Law we would have never hypothesised that blind cave fish could revert to an ancestral state. Thankfully, genetics supplied the framework from which the hypothesis flowed.
You never answered my question, Bill. Why do you suppose so many research papers are claiming that Dollo's Law has repeatedly been broken?
Comment by chunkdz — March 4, 2011 @ 9:04 pm
March 4th, 2011 at 9:11 pm
Chunkdz:
As my point regarding the inapplicability (x2) of your citation of Dollo's law in this instance stands whether Dollo was right or wrong, and I otherwise have no stake in it one way or the other, I'll leave that to others.
Comment by Reciprocating Bill — March 4, 2011 @ 9:11 pm
March 4th, 2011 at 10:32 pm
Reciprocating Bill:
Then if it's all the same with you I'm going to listen to what real published scientists say rather than what "Bill from the Swamp" sez. (Collin and Miglietta mention the cave-fish study as being an exception to Dollo's Law.)
I think I'll also ban you from this thread since twice you were too chicken to answer my simple question.
Oh yeah, chickens also violate Dollo's Law. That's in the article too.
Comment by chunkdz — March 4, 2011 @ 10:32 pm
March 4th, 2011 at 11:06 pm
Chicken? Why are chickens so ugly?
You would be too if you had a pecker in the middle of your face.
Comment by ID guy — March 4, 2011 @ 11:06 pm
March 4th, 2011 at 11:15 pm
Well that is your top-down view which is a philosophical/theological view. I have been trying to argue bottom-up that the scientific evidence as we presently understand supports that kind of meta-scientific interpretation. I think my analysis has been an objective one. However, our Darwinist critics here think that nature must be interpreted non-teleological so they only allow non-teleological interpretations even if there is evidence to the contrary.
Actually it appears that it is the sonic hedgehog gene interacting with the pax6 gene which is responsible for eye development in the Astyanax mexicanus somehow get switched off or inhibited when other adaptations that enhance the fishes survivability in a cave environment become more active. From a design perspective this makes perfect sense. The eyes are not needed and waste energy. On the other hand, Darwinists have to dismiss this adaptation as a lucky coincidence. KC even tried to argue that the loss of eyesight/eyes was not an adaptation at all. However, the Harvard study that I cited above argues otherwise.
The fact that eye loss is even partially reversible after a million years is absolutely amazing. There is in my view much more going on, on the genetic level than is presently understood. That is something that the committed Darwinist appears loathe to admit.
Comment by JOHN_A_DESIGNER — March 4, 2011 @ 11:15 pm
March 5th, 2011 at 12:19 am
JAD,
That's one part which stood out to me too – and what I found very interesting was how being able to recover eyesight in as little as 1 generation if crossed with a member of a long separated population was framed as an ability. I think there's something to be said for that. It suggests something about the underlying 'program', for lack of a better word.
Glad to see you guys found this as interesting as I did, despite its age. I didn't catch it the first time around, and I find it pretty fascinating.
Comment by nullasalus — March 5, 2011 @ 12:19 am
March 5th, 2011 at 12:38 am
The miracle of de-evolution.
Or would it be re-evolution?
Comment by Mung — March 5, 2011 @ 12:38 am
March 5th, 2011 at 12:41 am
Actually, it appears that there is LESS going on than is presently thought.
Comment by Mung — March 5, 2011 @ 12:41 am
March 5th, 2011 at 2:52 am
A festivus miracle of evolution!
Comment by kornbelt888 — March 5, 2011 @ 2:52 am
March 5th, 2011 at 7:03 am
No, John, I did not try to "argue that the loss of eyesight/eyes was not an adaptation at all". Whatever gave you that idea? I suggested we look at the blindness again and go over the evidence to make sure. That isn't arguing for it.
Comment by KC — March 5, 2011 @ 7:03 am
March 5th, 2011 at 8:48 am
Perhaps it wasn't a million years.
Just sayin'
Comment by ID guy — March 5, 2011 @ 8:48 am
March 5th, 2011 at 8:53 am
Since when is the theopry of evolution concerned with evidence especially when a glossy narrative works?
Comment by ID guy — March 5, 2011 @ 8:53 am
March 5th, 2011 at 8:57 am
Glad to see you guys found this as interesting as I did, despite its age.
Comment by fifth monarchy man — March 5, 2011 @ 8:57 am
March 5th, 2011 at 9:50 am
Whether or not blindness is an actual adaptation to a cave environment remains to be demonstrated. Protas et al (2007) is the "Harvard study" John referred to. They point out the energy cost of maintaining a retina (more specifically, the vertebrate retina) in the dark is higher than in the light. This can hamper an organism's ability to compete in a nutrient-poor environment (which is what I was hinting at when asking about common ecological characteristics of caves). So there is reason to think that mutations which reduce the maintenance of eyes could be selected for in cave environments, at least in vertebrates. But they present no work to actually demonstrate the selective effect on the trait itself.
On the other hand, Jeffery (2009) discusses evidence that mutations to sonic hedgehog gene regulation (and its downstream interaction with other genes) may be involved. He suggests that upregulation of sonic hedgehog results in eye regression, but, due to pleiotropic effects, may also enhance other traits (such as jaw development) which might be actually selected for in a cave environment. In this case, the eye regression, taken on its own, is not an adaptation. Instead, it is linked to another trait that is being selected for. The adaptive value of the other traits have not yet been established. There is also the possibility that all of the pleiotropic effects are beneficial and selected for. We just don't know yet.
Another thing we don't know is if the eye regression mutations occurred after the populations entered the caves. It's possible, for example, that upregulation of sonic hedgehog is part of the existing variation in surface populations, and its extreme effects may be the result of recombination with other genes (and selected against on the surface). So, instead of having to wait for individual mutations to occur in separate, isolated populations, recombination could produce the traits conducive to cave environments instead. Recombination is far more efficient than pure mutation pressure at producing variation. But that's just speculation on my part. I have no idea what the actual genetic makeup of the surface populations are, and if they are polymorphic for sonic hedgehog expression.
None of the above mechanisms preclude Darwinian explanations. If hedgehog genes are involved, and it's beginning to look more and more that they are, then the fact we also see eye regression in invertebrates in cave environments shouldn't be so surprising either, since the hedgehog gene family affects eye development in both groups.
Comment by KC — March 5, 2011 @ 9:50 am
March 5th, 2011 at 9:58 am
Oops. Here are the references:
Jeffery WR (2009). Evolution and development in the cave fish Astyanax. In Evolution and Development, WR Jeffery, ed. Elsevier.
Protas M, M Conrad, JB Gross, C Tabin & R Borowsky (2007). Regressive evolution in the Mexican Cave Tetra, Astyanax mexicanus . Current Biology 17: 452-454
Comment by KC — March 5, 2011 @ 9:58 am
March 5th, 2011 at 11:31 am
Lets not under-emphasize the role of preadaptation in these examples. It looks to me like many species of cave fish had ancestors that were already accustomed to feeding in the dark, they were already heavily relying on sense organs other than sight. I'd bet that this is a key reason why many species of cavefish do so well down there.
Comment by Guts — March 5, 2011 @ 11:31 am
March 5th, 2011 at 11:57 am
Guts writes:
It may not be a good idea to over-emphasize it either (my emphasis):
Romero A & SM Green (2005) The end of regressive evolution: examining and interpreting the evidence from cave fishes. Journal of Fish Biology 67: 3-32.
Comment by KC — March 5, 2011 @ 11:57 am
March 5th, 2011 at 12:16 pm
Yes, looks like being a generalist can also be important.
Comment by Guts — March 5, 2011 @ 12:16 pm
March 5th, 2011 at 12:57 pm
We're definitely on the same page here.
One thing I've repeatedly emphasized is that we all bring a philosophical view to the table and interpret the data according to that particular philosophy.
You can see that in action here as the "Darwinistas" try to make it sound like the restoration of eyesight, in one generation, from millions of years of blindness is a prediction of the ToE.
Amazing.
Comment by Daniel Smith — March 5, 2011 @ 12:57 pm
March 5th, 2011 at 1:30 pm
Nobody said that the restoration of vision in cave fish was a prediction of the Theory of Evolution. Except maybe in someone's imagination.
Comment by KC — March 5, 2011 @ 1:30 pm
March 5th, 2011 at 2:23 pm
Keep in mind that Darwin himself believed that the loss of eyes in cave animals is something that could not be explained by natural selection.
Here is a modern view that seeks an epigenetic explanation.
I also found this to be very interesting.
But modern Darwinists, breaking even with Darwin, insist that there must always be a Darwinist explanation.
Early in this discussion I pointed out that the term orthodoxy was a quasi-religious term. Now that the discussion has evolved we find that behind the Darwinian orthodoxy there is blind faith and dogmatic belief as deep and irrational as we find in the most irrational kinds of religion. Darwinism must be true even if there is evidence to the contrary. It must be believed apparently because the alternative, that nature is teleological, is unthinkable.
Comment by JOHN_A_DESIGNER — March 5, 2011 @ 2:23 pm
March 5th, 2011 at 3:46 pm
KC wrote:
Ahem. Below, emphasis mine:
Reciprocating Bill wrote:
This finding sits neatly within an orthodox evolutionary framework. Most important, going to the original paper, it is notable that this research was conducted to test a prediction arising out of that framework, as well as previous observations regarding the results of hybridization. That's how science is done.
Sorry, you lose the Internet.
Comment by angryoldfatman — March 5, 2011 @ 3:46 pm
March 5th, 2011 at 4:50 pm
angry old fat man,
Bill did not say that the theory of evolution predicted that the vision would be restored. The research on cave fish was conducted within an orthodox evolutionary framework, some of which consists of predictions made by evolutionary theory itself, some not. For example, evolutionary theory does predict that isolated populations will diverge genetically from each other, due to the nature of mutation and recombination. From that , the researchers predicted that vision might return in hybrids between those isolated cave populations due to complementation. Evolutionary theory predicted divergent mutation patterns. It is the principle of complementation (which isn't evolutionary theory) that predicts the trait will revert.
So, the only way Reciprocating Bill could have actually meant evolutionary theory predicted the return of vision would be if he was strictly equating "evolutionary framework" with "evolutionary theory", which I doubt. We could ask him specifically, I suppose, but chunkdz may have prevented him from answering:
Comment by KC — March 5, 2011 @ 4:50 pm
March 5th, 2011 at 7:25 pm
If an evolutionary framework does not fit in the Theory of Evolution, then it is not orthodox. That's what the Theory of Evolution consists of – a set of orthodox evolutionary frameworks.
An UNorthodox evolutionary framework would be something like Intelligent Design or Morphogenic Fields. These do not fit in the Theory of Evolution as the term is currently understood.
You lose another Internet. You're running out of Internets quickly here.
Comment by angryoldfatman — March 5, 2011 @ 7:25 pm
March 5th, 2011 at 7:31 pm
And I don't care about Reciprocating Bill excepting his assertion disproving your asinine claim. Anybody who wants to cry and wail and rend their garments over somebody else getting banned from one thread needs to HTFU.
Language warning on the link.
Comment by angryoldfatman — March 5, 2011 @ 7:31 pm
March 5th, 2011 at 8:13 pm
Comment by KC — March 5, 2011 @ 8:13 pm
March 5th, 2011 at 8:25 pm
And anyone who has nothing better to offer than phony postmodernist word gaming to offer should go join Daniel making bumper sticker slogans. Poseur.
Comment by KC — March 5, 2011 @ 8:25 pm
March 6th, 2011 at 1:09 am
I have little to add to this amusing argument other than to say it's been my anecdotal experience that self-proclaimed "Darwinists" tend to be as guilty of the word-gaming charge than anyone else. Pot, kettle, and all that.
And really, that does seem to be a charge leveled here with Dollo's law itself. That exceptions and falsifications become non-exceptions by means of word games. Is that charge accurate? I leave that to present company to discuss, for now.
I do urge everyone to be polite and civil, though. No sense getting too animated over this. And I can't help but add, "Poseur? Really? Is AOFM 'major uncool' too?"
Comment by nullasalus — March 6, 2011 @ 1:09 am
March 6th, 2011 at 9:54 am
Well, the biggest problem was calling it a "law" in the first place. The term implies universal applicability without exception. But even laws have to bend to reality, especially as new data comes in. And finding exceptions to them doesn’t necessarily mean they no longer hold generally. Newton’s Laws of Motion come to mind as a classic example. Newton’s Laws of Motion apply universally, except when they don’t ( when rigid bodies are involved, or near the speed of light). That doesn’t mean they aren’t still useful as general principles under certain conditions. The situation is no different with Dollo’s Law.
Now, at one point in the discussion both Reciprocating Bill and I pointed out that Dollo’s “Law” did not apply in the case of the return of cave fish vision. That sparked some skepticism, even derision. But let’s look at what Dollo himself had to say (my emphasis):
Dollo is clear—by reversability he means retracing all of the steps that brought about the trait in the exact order in which they occurred. So, when we look at the paper under consideration, were those steps traced exactly? No. For one thing, retracing the exact set of circumstances would have to involve only the lineage in which the steps occurred. The simple fact that different lineages were used for the hybridization immediately invalidates applying Dollo’s law. Never mind that the exact set of mutations that caused the vision loss were not reversed, nor were they reversed in the same order in which they occurred.
So, null, its very clear that the work done restoring vision in cave fish is not an exception to Dollo’s Law. We can see this clearly from the man’s own description of his principle.
Comment by KC — March 6, 2011 @ 9:54 am
March 6th, 2011 at 9:58 am
Well, he did try and use the hip "HTFU" expression., like an Internet Tough Guy.
Comment by KC — March 6, 2011 @ 9:58 am
March 6th, 2011 at 2:45 pm
What do you think angryoldfatman?
I think we could make a killing!
Comment by Daniel Smith — March 6, 2011 @ 2:45 pm
March 6th, 2011 at 3:10 pm
Daniel Smith wrote:
It'd be more fun than fixing computers for a living, that's for sure.
Then again, so is getting KC to lapse into profanity by simply pointing out the deficiencies in his argument.
KC wrote:
u mad bro?
y u no think ToE include all orthodox evolutionary framework?
Comment by angryoldfatman — March 6, 2011 @ 3:10 pm
March 6th, 2011 at 3:34 pm
Oh and by the way, KC, there's nothing rhetorical or post-modern about the serious portion of what I've written. Your claim and my counter could be fairly easily illustrated with Venn diagrams.
Either the ToE is a superset of orthodox evolutionary frameworks or it isn't. If it isn't, then the orthodoxy of the ToE is in question, since there are orthodox evolutionary frameworks that somehow lie outside of it.
A possible rebuttal of yours (if I comprehended your only relevant reply to me) to would be that there are orthodox evolutionary frameworks that are not truly subsets of the ToE, but that these sets share large intersections, with part of the orthodox frameworks being outside the ToE.
This position would make front-loaded evolution (FLE) an orthodox evolutionary framework. The portion of FLE that involves a designer doing the front-loading is obviously outside of the ToE, while all of the rest is neatly tucked inside the ToE.
So if you still want to hang your hat on your initial claim that started this whole dust-up, then I have to ask you: do you believe FLE is an orthodox evolutionary framework, and if not, why not?
Comment by angryoldfatman — March 6, 2011 @ 3:34 pm
March 6th, 2011 at 5:04 pm
What Dollo seems to be saying is that in order for organisms to re-acquire a trait they lost, he thinks some exact duplication of steps would be necessary, therefore species don't re-acquire traits. But, organisms do re-acquire traits. Therefore, etc. That still seems like another way of pointing out that Dollo's law is wrong.
But, maybe you have a cite where Dollo spells out conditions under which he thinks organisms could re-acquire traits?
Comment by nullasalus — March 6, 2011 @ 5:04 pm
March 6th, 2011 at 8:00 pm
The pleiotropic effect is when a single gene influences multiple phenotypic traits. For example in the case of A. mexicanus, the cave fish we have been discussing, the same gene that’s been implicated in the loss of eyes also causes an “increase in feeding apparatus (jaws, teeth, taste buds) and body fat content… Yamamoto et al. (Yamamoto et al., 2004) have shown that eye regression is a consequence of early overexpression of hedgehog genes (Hh, including Shh) at the ventral midline of cavefish embryos.”http://dev.biologists.org/cont...
Luis Espinasa worked in Jeffery's laboratory shortly after the publication of the momentous work on lens transplants. Espinasa's research was focused…
But how does this pleiotropic effect evolve in the first place? Is a blind irrational process like natural selection really that clever?
Some of the literature makes it sound like the loss of eyes is a coincidence, a side effect or an accident. For example, Espinasa writes up above, “Natural selection is not acting on cave-fish eyes; it is acting instead to increase the fish's sense of smell.”
How in the world would he know that?
What about all the other eyeless cave animals (insects, worms, crayfish, salamanders) which have evolved that way independently over an over again? Just a coincidence or accident?
Of course that is where you end up if you follow Darwinian thinking to it’s logical conclusion.
In his 1985 book, Evolution: A Theory In Crisis, Michael Denton has a chapter entitled “The Priority of the Paradigm.” It was a critique of what happens when people make Darwinian evolution the orthodox position.
As an intelligent agent I can understand why cave animals have lost their eyes. They are no longer needed.
Comment by JOHN_A_DESIGNER — March 6, 2011 @ 8:00 pm
March 6th, 2011 at 9:06 pm
Despite the confidence that the theory of evolution’s so called modern synthesis evokes there are still major area’s of difficulty.
For example, biologists have been able to say with some confidence, that forms change, and that natural selection is an important force for change. Yet they have been able to say virtually nothing about how that change is accomplished. How bodies or body parts change, or how new structures arise. That has remained a complete mystery.
Comment by JOHN_A_DESIGNER — March 6, 2011 @ 9:06 pm
March 6th, 2011 at 10:47 pm
AOFM,
Venn diagrams can make everything look all mathematical and sciency and stuff, but they simply aren’t necessary for this discussion. Reciprocating Bill explained what he meant by “orthodox” when he said the prediction came out of an orthodox evolutionary framework. He meant “mainstream” (he even explicitly said so, so nobody has any excuse to misconstrue what he meant) By framework both he and I mean simply the palette of biological sciences (Genetics, Molecular Biology, Ecology, Physiology, Zoology, Botany, Paleontology, etc) with Mainstream Evolutionary Theory to tie it all together. If that wasn’t clear enough before, it should be crystal clear now. As I wrote earlier about the paper in question, the prediction that vision might be restored in the hybrids comes directly from the principle of complementation, which is straightforward Genetics. Nick pointed this out as well, so nobody has any excuse to misconstrue that, either. Mainstream evolutionary theory does not specifically make the prediction. What it does predict is that isolated lineages will diverge genetically by accumulating different sets of mutations. This gave the authors reason to hypothesize that the differences responsible for loss of vision among those lineages could be complementary. The prediction from that hypothesis was that vision could be restored in hybrids via complementation. But the prediction was not a prediction of mainstream evolutionary theory. My initial statement still stands.
Similarly, IDers could use their own FLE framework from which to make predictions. Maybe FLE itself specifically predicts that vision in cave fish will be restored by hybridization. I dunno. From what I understand of FLE, however, I don’t think it does any more than mainstream evolutionary theory does.
Comment by KC — March 6, 2011 @ 10:47 pm
March 6th, 2011 at 11:00 pm
Well, when we say they "reacquire" traits, we need to make sure just what we mean. Do we mean simply a phenotype that resembles the original? If so, what if the underlying set of mutations for the original is not the same set that underlies the "reacquired" trait? Is it truly an exception to Dollo's Law? Or is it just an example of another way to skin a cat?
Comment by KC — March 6, 2011 @ 11:00 pm
March 6th, 2011 at 11:34 pm
I think we need to make sure what Dollo meant first.
I asked if Dollo ever gave conditions under which one could expect the reacquisition of lost traits. Where is that? That would help, at the least.
Or hey, maybe Dollo never gave such an outline. I suppose that's possible too.
Comment by nullasalus — March 6, 2011 @ 11:34 pm
March 7th, 2011 at 12:47 am
KC wrote:
So you think I didn't know the colloquial meaning of the term "orthodox" and that was the definition being used.
Fine. Let us substitute the word "mainstream" for "orthodox" and see if everything still applies.
Either the ToE is a superset of mainstream evolutionary frameworks or it isn't. If it isn't, then the acceptance of ToE as mainstream in question, since there are mainstream evolutionary frameworks that somehow lie outside of it.
A possible rebuttal of yours (if I comprehended your only relevant reply to me) to would be that there are mainstream evolutionary frameworks that are not truly subsets of the ToE, but that these sets share large intersections, with part of the mainstream frameworks being outside the ToE.
This position would make front-loaded evolution (FLE) a mainstream evolutionary framework. The portion of FLE that involves a designer doing the front-loading is obviously outside of the ToE, while all of the rest is neatly tucked inside the ToE.
Wow, you're right. No, wait… nope, not one lick of difference. Mainly because I read how "orthodox" was being used in the thread. Sorry Charlie.
According to what you've stated above, gradual divergence is predicted by ToE, but not sudden convergence (not surprising, since they're diametrically opposed).
That makes Dollo's Law mainstream, but not this principle of complementation you've mentioned. So complementation does NOT fall neatly into a mainstream evolutionary framework as Bill said it did.
It seems you're saying Bill was wrong; if so, then you have my full agreement. If you still contend that Bill was correct AND that the complementation principle falls partially outside of the ToE, then you are contradicting yourself.
The only reason you support Bill is because of his rhetorical attempt to counter the obvious problem you're alternately confirming and denying. He tried the old "this exception is actually proof that Darwinian evolution is true" trick, which he blindly rode right into the path of the banhammer.
The funny thing is that by doing so, you've pretty much admitted that the ToE is useless and outdated, even equating it with an ID-tainted hypothesis.
Like I said before, the comedy writes itself.
Comment by angryoldfatman — March 7, 2011 @ 12:47 am
March 7th, 2011 at 6:53 am
I don't know, null. The quote I gave was from a paper citing him. His original papers are in French. Gould wrote an essay about him, I may go look that one up (It's not available online).
Comment by KC — March 7, 2011 @ 6:53 am
March 7th, 2011 at 8:08 am
Null,
In the meantime, I did find this Dollo quote from 1893:
Comment by KC — March 7, 2011 @ 8:08 am
March 7th, 2011 at 10:56 am
Heraclitus said, “You can never step in the same river twice.”
It seems to me that Dollo’s law is just philosophy dressed up as science.
Comment by JOHN_A_DESIGNER — March 7, 2011 @ 10:56 am
March 7th, 2011 at 12:52 pm
San juan capistrano has it swallows, Hinckley, Ohio, which is close to where I live, has some Buzzards that allegedly return, like clock work, every year on March 15th . A few years ago a local TV station interviewed one of the Park Rangers, who worked at the Hinckley Reservation, whether the Buzzards ever return earlier. “Nope,” the Ranger said, “We know that they don’t, so we don’t even bother to look.”
Of course, the Ranger's flippant tongue-in-the-cheek response (I sensed that he knew something we don’t know) is a classic example of circular reasoning. And, when I comes to preserving traditions, like the return of the buzzards, this kind of reasoning, in my opinion, is really quite innocent. On the other hand, if you are doing scientific research it an entirely different matter.
For example, here is Jerry Coynes thinking on new research into “epigenetics.”
In other words, Coynes reasoning is, we already know what the major driver in evolution is, natural selection (NS + RV), so why even bother considering anything else?
I would say that Coyne is committed to some kind of orthodox interpretation of evolution. Is it his orthodoxy, or is it an orthodoxy that is widely shared among evolutionary biologists? Is the standard operating procedure in evolutionary biology to apriori reject any hypothetical explanation that is outside the mainstream?
I say this because it seems to me to be at least possible that the eyelessness we observe over-and-over in cave animals could be an environmentally-induced epigenetic change and not the result of natural selection. Exactly who or what does it hurt to consider that kind of hypothesis?
BTW I would argue that the above is not necessarily an ID hypothesis, however, it is an explanation that is clearly outside the mainstream.
Comment by JOHN_A_DESIGNER — March 7, 2011 @ 12:52 pm
March 7th, 2011 at 3:44 pm
KC:
I think you're wrong. Here's why.
Dollo used the word 'steps' without even knowing what a 'step' was or how steps are taken. Dollo was a saltationist, so he would not have a problem conceptually with those steps being "organism loses vision gene" or it's exact reverse, 'organism regains vision gene' (if he knew what a gene was, that is). Exact steps, as far as a 19th century naturalist is concerned.
It does no good for you to invoke the fact that the mechanism for the reversal is not what was expected, because Dollo himself never specified the mechanism because Dollo had NO CLUE as to what the mechanism might be. He just looked at fossils and organisms and basically said "Nope, too complex. Ain't gonna happen".
As an ID critic you should be keenly aware of the pitfalls of complexity arguments from incredulity.
Comment by chunkdz — March 7, 2011 @ 3:44 pm
March 7th, 2011 at 4:37 pm
angryoldfatman:
Suppose I take a black mouse and an albino mouse and breed them. The offspring are all black. Was the trait of albinism lost in an evolutionary sense? Now breed two of the F1 generation. In the F2 generation, you have 25% albino mice. Did albinism suddenly re-evolve in the population? Set up two pairs of F1 mice. In both cases, the black parents produce 25% albino pups. Is the presence of albino pups in both litters an amazing example of sudden convergence?
Basically, you are making a category error. Mendelian genetics, including complementation of nonallelic mutations, is not the same as (or a subset of) evolutionary convergence. Complementation of nonallelic mutations is consistent with a standard evolutionary framework. I'm sure it fits well in a FLE framework. It might even fit well in a YEC framework, if YEC were well developed enough to include genetics. That's not to say Reciprocating Bill was wrong in his claim that the authors of the study in question made a prediction based on mainstream evolutionary science. He was clearly right about that.
Comment by Nick — March 7, 2011 @ 4:37 pm
March 7th, 2011 at 4:45 pm
John A Designer:
Have you read the papers that started this discussion? The results demonstrate that the alleles controlling the eyelessness phenotype are inherited in a Mendelian fashion. That rules out an epigenetic origin for the phenotype (though there could be minor epigenetic effects playing around the edges, I suppose).
Heck, you could demonstrate it for yourself, if you are so inclined. Blind cave fish are common aquarium fish, as are their wild-type, surface dwelling ancestors. Buy a few and breed them in an aquarium. Note how the trait disappears and reappears in subsequent hybrid generations. That's genetics, not epigenetics.
Exactly who or what does it hurt to consider that kind of hypothesis?
Well, for one thing, it's a waste of grant money when the answer is already known.
Comment by Nick — March 7, 2011 @ 4:45 pm
March 7th, 2011 at 5:59 pm
Nick,
Other research would argue that the science is far from settled here.
In chapter 15 of his book Cabej concludes:
It's important to consider all the questions and look at all the evidence, not just cherry pick what you like.
Comment by JOHN_A_DESIGNER — March 7, 2011 @ 5:59 pm
March 7th, 2011 at 6:49 pm
I think one problem I'm having here comes down to this: We have 'Dollo's law', and then we have 'people who interpret Dollo's law'. When conflicts are found to the 'law' as plainly stated, they get treated either as contradictions (Dollo's law doesn't hold here, violation found) or as exceptions (Dollo's law was never meant to hold here, no violations found.)
Comment by nullasalus — March 7, 2011 @ 6:49 pm
March 7th, 2011 at 7:19 pm
Mendel was a creationist, so it is a given YEC includes genetics. Heck under YEC recombination is basically the only way to get the allele distribution we observe today in humans from two people.
I am sure YECs understand that genes influence traits and development. So I am not sure what you are talking about but that is a discussion for another thrad at some other time.
Comment by ID guy — March 7, 2011 @ 7:19 pm
March 7th, 2011 at 7:37 pm
Pop quiz: Who said this?
Comment by JOHN_A_DESIGNER — March 7, 2011 @ 7:37 pm
March 7th, 2011 at 7:46 pm
Fixed that for you KC!
(Sorry – it was too long to fit on a bumper sticker.)
Comment by Daniel Smith — March 7, 2011 @ 7:46 pm
March 7th, 2011 at 7:54 pm
nullasalus:
I think it's important to realize that if Dollo had ever encountered the fish from this study he would never have concluded that it had ever lost it's eyesight. And he certainly never would have predicted that breeding two blind fish would create sighted fish.
In fact, he likely would have concluded much the opposite. Such is the much vaunted and non-existent Theory of Evolution.
Comment by chunkdz — March 7, 2011 @ 7:54 pm
March 7th, 2011 at 11:30 pm
Here is another perspective of the notorious Altenberg 16 that conference that Susan Mazur wrote about, originally published in AAAS’s Science Magazine by staff writer Elizabeth Pennisi in 2008.
It sounds to me like there are some prominent non-ID scientists and philosophers who are dissatisfied with the orthodox interpretation of the modern synthesis.
Comment by JOHN_A_DESIGNER — March 7, 2011 @ 11:30 pm
March 7th, 2011 at 11:36 pm
JAD,
A side anecdote. One time I was talking with someone who was angrily denouncing ID, and in particular was challenging the ID criticisms of Neo-Darwinism. At one point, they linked to the blog of a biologist who had some very critical things to say about ID.
So I checked out the link. Whaddya know – it's Allen MacNeill.
Once I started mentioning MacNeill's views on neo-darwinism, the man who was for this person a citeworthy expert an hour ago suddenly became someone whose opinion meant nothing.
I bring this up for two reasons: One, I think it's a funny story. Two, I suspect many people would agree with Pennisi. The trick is to revise the modern synthesis while pretending you aren't.
Comment by nullasalus — March 7, 2011 @ 11:36 pm
March 8th, 2011 at 12:45 am
nullasalus,
Probably no theory in physics has been has been better established than has Einstein’s theory of general relativity. Yet there is a big flaw…
The irony is that no gets upset when we point out, paraphrasing Eva Jablonka, that a new theoretical synthesis in physics is long overdue. And as we know even Einstein would have agreed with that.
What is it about evolution that gets people so emotional? It would be nice sometime just to have an adult conversation about the modern neo-Darwinian synthesis strengths and weaknesses. Of course that means you have to find some adults with whom to have a conversation.
Comment by JOHN_A_DESIGNER — March 8, 2011 @ 12:45 am
March 8th, 2011 at 1:12 am
Some months ago an American philosopher explained to a highly sophisticated audience in Britain what, in his opinion, was wrong, indeed fatally wrong, with the standard neo-Darwinian theory of biological evolution. He made it crystal clear that his criticism was not inspired by creationism, intelligent design or any remotely religious motivation. A senior gentleman in the audience erupted, in indignation: ‘You should not say such things, you should not write such things! The creationists will treasure them and use them against science.’ The lecturer politely asked: ‘Even if they are true?’ To which the instant and vibrant retort was: ‘Especially if they are true!’ with emphasis on the ‘especially’.
Not that this is news to you, or anyone else here. But oh, what a perfectly quotable moment.
Comment by nullasalus — March 8, 2011 @ 1:12 am
March 8th, 2011 at 6:58 am
Cafe Press sells t-shirts and coffee mugs too
Comment by KC — March 8, 2011 @ 6:58 am
March 8th, 2011 at 10:11 am
John A Designer:
Indeed. So, have you looked at the papers on Astyanax that Cabej cites, or are you basing your opinion on the cherry-picked quotes in his posting?
The 2005 J. Heredity review by W.R. Jeffery that Cabej quotes selectively is very interesting if you want to know whether cave fish evolution is likely to be driven by natural selection or neutral mutations, but the gene expression data and transplantation experiments described in the review are not informative with regard to epigenetic origin or expression of the traits.
Most of the data in the review by Romero and Green is likewise not informative with regard to epigenetics. The paper contains a very brief (one sentence) discussion of how epigenetics may affect phenotypic plasticity, but that is in context of genotype-specific reactions. In other words, the precise phenotype of a "troglomorphic" fish may vary due to environmental effects, some of which might have epigenetic components, but what distinguishes a troglomorphic fish from a surface dwelling "epigean" fish is its genotype. By analogy, consider Randy Jirtle's work on the viable yellow allele in mice. Mice with the viable yellow genotype have a variable phenotype due to epigenetic effects, but what distinguishes viable yellow mice from wild-type mice is an insertional mutation. In other words, the origin of the viable yellow allele is genetic, not epigenetic.
So, again, while there could be epigenetic effects playing around the edges of the troglomorphic (I love that word!) phenotype, the evidence taken as a whole indicates that the evolutionary origins of the various traits are genetic.
Comment by Nick — March 8, 2011 @ 10:11 am
March 8th, 2011 at 12:05 pm
null,
I think the problem is slightly different. If we take Dollo's own words, then his law applies only to exactly reacquiring the trait as it was before, and in exactly the same order. The problem comes when we look at Dollo's law in the light of modern genetics. Since Dollo formulated his "law" before Mendels work had been rediscovered (let alone integrated into evolutionary theory), should we include the exact mutational path as a requirement for Dollo's Law? If we do, then it is clear that the hybridization/complementation breeding experiments would almost certainly not apply, and are therefore not an exception to the law. But what about some of the other cases? If all we are doing is observing a morphological feature reappear, in order to decide if it's an exception to Dollo's Law under the strict interpretation, then we have examine the underlying genotype and the path it took to reacquire the trait, and if it's different then it is not an exception to the law.
My question is, who gives a tinker's damn if such a strict interpretation of the law is used or not? Like Newton's Laws of Motion, Dollo's Law does have a general use despite exceptions– it's still true that reacquisition of a lost trait becomes more difficult the more mutations there are involved. Dollo's Law doesn't have to be universally true to still embody this basic principle.
Comment by KC — March 8, 2011 @ 12:05 pm
March 8th, 2011 at 1:31 pm
Nick,
Nature News in 2008 reported:
Are you a researcher? How would you know what they do not know? An a priori commitment to neo-Darwinism?
You seem to me to be arguing that natural selection acting on random mutation happens by chance to create the same adaptation over-and-over again. Indeed, the research shows that this adaptation has occurred independently several times (at least four) A. mexicanus but that similar adaptations have occurred in other troglomorphic (cave dwelling) fish and animals. That’s like rolling a handful of dice and coming up with ones and sixes most of the time. If I observed something like that I would suspect that the dice are loaded. I don’t think neo-Darwinism presented as a non-falsifiable hypothesis is a good explanation here.
As far as Romero and Green not being very informative with regard to epigenetics. You apparently did not notice figure 15.20 of the Cabej link that I provided. Here is the text:
The morphological changes induced by exposure to light are clearly epigenetic in nature.
I don’t know if an epigenetic explanation is the answer here. Indeed I will concede there are number of thing we don’t as yet understand. I just think it’s worth looking into because it is both a possible and scientifically plausible explanation.
PS Do you have an answer or guess for my pop quiz?
Comment by JOHN_A_DESIGNER — March 8, 2011 @ 1:31 pm
March 8th, 2011 at 2:52 pm
John A Designer:
I didn't claim to know exactly what drives the evolution of the cave phenotypes. I claimed that there was sufficient data to rule out an epigenetic explanation for their origin. Can you see the logical difference between those two statements.
After lecturing me on the importance of looking at all the evidence and not cherry picking, you are still posting out-of-context snippets of news reports. The irony is that the Nature News article describes Borowsky's research demonstrating the genetic basis of the traits.
The morphological changes induced by exposure to light are clearly epigenetic in nature.
The morphological changes induced by exposure to light may be epigenetic in nature, but that doesn't explain the origin of the troglomorphic forms. Look more closely at Romero and Green's figure. The two parent forms and the hybrids show an effect of environment on phenotype, but they are constrained by genotype. Light does not convert a troglomorphic fish into an epigean fish (and an increase in melanophores does not equate to functional eyes). A troglomorphic genotype is required to generate a troglomorphic phenotype — which gets us back to Borowsky's genetic data. An epigenetic explanation for the origin of troglomorphic forms is only plausible if you ignore the genetics.
Furthermore, Borowsky and colleagues have started to identify the specific mutations in the genes underlying the troglomorphic phenotypes. See Gross et al (2009) PLoS Genetics 5:e1000326.. Following up on their hybridization and genetic mapping experiments, the authors identified two mutations in the Mc1r gene. One of the mutations is an premature stop codon and the other an amino acid substitution. As predicted, fish from different cave systems have different mutations. When the actual mutations are identified, there's not much room left for an epigenetic origin of the trait.
I had no guess, so I googled it. Now that I know, I am none the wiser. Can you tell us why it is significant who said that?
Comment by Nick — March 8, 2011 @ 2:52 pm
March 8th, 2011 at 3:40 pm
Chunk,
Sorry, I missed your earlier comment. I wasn't trying to ignore it.
Maybe not genetic steps. But it would be a mistake to assume that Dollo was not sophisticated enough to look at it probabiistically given what he had to work with (he was initially trained in engineering and mathematics). If a complex morphological feature requires a large number of stages or steps in a certain order to complete (as could be seen revealed over time in a successive fossil lineage), then it could be argued that the probability of exactly retracing those steps would be less than that for a trait that required very few. In fact, a good engineer could see how certain series of steps could be more physically constrained and thus harder to achieve than others.
A very interesting modern use of this kind of analysis was done by Gould and Robinson in 1994, and I doubt Dollo would have had any trouble with it:
From the abstract:
Gould SJ & BA Robinson (1994).The promotion and prevention of recoiling in a maximally snaillike vermetid gastropod: a case study for the centenary of Dollo's Law. Paleobiology 20(3): 368-390.
Of course. I am also keenly aware of the pitfalls of assuming an argument from incredulity is being made when it isn't.
Comment by KC — March 8, 2011 @ 3:40 pm
March 8th, 2011 at 5:59 pm
And I think JAD is right in calling that work of the words out as ridiculous. It turns Dollo into freaking Heraclitus. It's almost as bad as labeling any model of evolution as Darwinian so long as natural selection played any role at any time in any place in the history of the universe. A trait was lost. It was reacquired. Yes, Dollo did not foresee this, and was not aware of genetics. As I said earlier, that's just another way of noting Dollo was wrong.
The guys insisting Dollo's law hasn't really failed to hold, for one. That's like asking "Who cares if Darwin got something wrong?" A surprising number of people, as a matter of fact.
Comment by nullasalus — March 8, 2011 @ 5:59 pm
March 8th, 2011 at 7:27 pm
Nullasalus:
KC:
Sigh…
I don’t know about anybody else, but I’m getting sick and tired of calling something a law just because some old guy happened to dream it up.
According to Ernst Mayr there is only one law in biology namely that “THERE ARE NO LAWS IN BIOLOGY…”
I think we should follow Mayr’s advice, not because he was some old guy, but because he was an important old guy who didn’t like laws.
Comment by JOHN_A_DESIGNER — March 8, 2011 @ 7:27 pm
March 8th, 2011 at 8:28 pm
KC:
Reality is that the steps ARE genetic steps. If your argument is that Dollo's Law does not apply to reality, then so be it.
It's not that Dollo lacked sophistication. He lacked knowledge of how sophisticated life is.
And a better engineer could see life as a systems engineering project wherein systems can get turned off or shut down for millions of years then get reactivated. This points out another of Dollo's mistakes – looking at evolution as a mathematical reduction rather than a holistic program.
Yes, sometimes organisms can almost revert to a former state. And sometimes they can completely revert to a former state. And sometimes they can't revert to a former state.
So show me the predictive power of Dollo's Law. Which ancestral states are achievable from current states and why? Until then Dollo's Law is just observation from an uninformed perspective.
Why stop there. Let's insist that the spin of each electron must exactly match the original. You know, whatever it takes to salvage Dollo's reputation.
Sorry, KC, but you must realize how silly it sounds to insist that Dollo's Law applies to evolution – as long as cave fish don't have sex.
Comment by chunkdz — March 8, 2011 @ 8:28 pm
March 8th, 2011 at 10:39 pm
Chunk,
No sillier than to insist Newton's laws of motion apply to planetary motion– as long as the planets are idealized as tiny particles that don't move TOO fast.
Funny, I don't see any of you getting in physicists' grills about that.
Comment by KC — March 8, 2011 @ 10:39 pm
March 8th, 2011 at 11:10 pm
Physicists are usually willing to admit that Newton's Rape Manual was incorrect about this or that.
Comment by nullasalus — March 8, 2011 @ 11:10 pm
March 8th, 2011 at 11:55 pm
I see. So Dollo was simply ignorant of the mysterious and unknown ethereal realm known as…. sexual reproduction!!
Comment by chunkdz — March 8, 2011 @ 11:55 pm
March 9th, 2011 at 7:49 am
Null,
I don't see biologists losing sleep over Darwin being wrong about gemmules. Do you?
Comment by KC — March 9, 2011 @ 7:49 am
March 9th, 2011 at 8:08 am
chunk,
The usefulness of Dollo's Law as a rhetorical cudgel against mainstream evolutionary theory has clearly diminished, now that everyone realizes it has exceptions, and still has use as a general principle when considering the types of constraints on the direction evolution can take in a lineage (see Gould & Robinson's paper for an excellent discussion of the issues).
We are left with comments that Dollo was a crappy engineer, that he was no more useful to biology than Heraclitus, and that old men shouldn't come up with laws that don't have universal, absolute applicability (especially if they can't be used to bash mainstream evolutionary theory).
LOL.
Comment by KC — March 9, 2011 @ 8:08 am
March 9th, 2011 at 11:01 am
You were probably assuming that I was referring to some famous or prominent scientist. Actually I thought the quote and article were interesting not because of who Andrew Howley is but because of who he works for– National Geographic.
National Geographic from my experience has usually been in the tank for neo-Darwinism. However, in his article, “Epigenetics: How Evolution Is Evolving,” Howley makes a stunning departure from neo-Darwinian thinking. Notice how he begins:
He then goes on to write:
Basically, that is what Cabej has been suggesting in regards to the evolution cavefish and other cave dwelling animals.
I don’t see that you are in the position to rule out epigenetics a priori considering that epigenetic research is still in it’s infancy. I think there is more than enough evidence in this case to warrant further study.
Comment by JOHN_A_DESIGNER — March 9, 2011 @ 11:01 am
March 9th, 2011 at 11:51 am
John A Designer:
I didn't rule it out "a priori." I ruled it out on the basis of the published experimental data clearly demonstrating the genetic, not epigenetic, basis of the troglomorphic phenotype in Astyanax.
Comment by Nick — March 9, 2011 @ 11:51 am
March 9th, 2011 at 12:17 pm
I wrote:
Correction to my last post:
the word "basis" should be "origin."
I suspect that we are reaching the point of diminishing returns in this discussion, so I'll summarize my position and let you have the last word.
1. If the troglomorphic form of Astyanax has an epigenetic origin, troglomorphic and surface fish should be genetically equivalent (that's the whole point of epigenetics).
2. Conversely, if the troglomorphic forms has a genetic origin (i.e. mutation), the troglomorphic and surface fish will be genetically distinct.
3. The experiments in the papers that we have been discussing demonstrate that the troglomorphic traits are linked to particular genetic loci. The results of the complementation tests that started this whole thread point to the troglomorphic traits being genetically defined, with different cave populations carrying different mutant alleles. Therefore, the evidence supports 2 (genetic origin) not 1 (epigenetic origin).
4. But that's not all. The most recent published experiments identify genetic mutations linked to one of the troglomorphic traits. The authors went even further and produced a similar phenotype in a different species by altering the same gene. That result confirms the mutations are the cause of the trait.
5. Phenotypic variability under different evironments is not clear evidence that the a trait has an epigenetic origin, despite what Cabej might claim. What the totality of the cavefish data indicates is that the traits are caused, genetically, by mutations in a variety of genes, but the specific phenotype deriving from those mutations is modulated by environmental factors. But the bottom line is, no mutations, no troglomorphic fish.
Comment by Nick — March 9, 2011 @ 12:17 pm
March 9th, 2011 at 2:06 pm
KC:
As well as it's "orthodoxy" in mainstream evolutionary theory.
(If there was such a thing as mainstream evolutionary theory, that is.)
Comment by chunkdz — March 9, 2011 @ 2:06 pm
March 9th, 2011 at 3:31 pm
If you are not to even willing to consider the possibility then you are indeed dismissing the idea a priori. I think it is possible that some of the analysis of the data is skewed here because an epigenetic explanation was not even considered. However, due to the newness of epigenetics I am willing to cut them some slack.
Comment by JOHN_A_DESIGNER — March 9, 2011 @ 3:31 pm
March 9th, 2011 at 7:57 pm
KC,
I don't see anyone talking about gemmules, period. But the last time we saw articles running with the claim that research showed Darwin was wrong about competition driving natural selection, some pants were being shat over at the NCSE. Same when it was claimed that Darwin was wrong about the tree of life.
Go back to the Piatelli-Palmirini quote. It's not Darwin being wrong on this or that that's the problem for a lot of people. It's saying he's wrong in public. Likewise, it's not orthodox evolutionary theory being wrong on this or that that's the problem for many. It's the stating in public that that was the case that is the problem.
So yeah, if it were pointed out in the right venue that Darwin was wrong about gemmules, I would not be too surprised to see something similar to the Dollo card being played there.
Comment by nullasalus — March 9, 2011 @ 7:57 pm
March 9th, 2011 at 8:31 pm
Here are several quotes from one of W.R. Jeffry’s papers that suggest to me that we still do not know enough about the evolution of the cave dwelling fish A. mexicanus to rule out an epigenetic explanation for the adaptations we observe.
How can random mutation explain the fact that “eye degeneration is controlled by the same or similar mechanisms in different cavefish populations” that appear to have evolved independently of each other?
What we know at present is that a signaling gene, the sonic hedgehog (shh) gene, is that it is an up-regulated gene and because of the pleiotropic effect causes a reduction of the pax6 gene which effects eye development. In other words, eyeless fish still have the genes for eyes but their development is arrested part way through embryonic stage. The question is, in my mind, what causes the shh to be up-regulated? Is it because of a mutation, or because something in the environment? My initial and very cursory survey of the literature available on-line is that it could be environmental… Why in the world would we not want to investigate that further?
Ruling out a scientific hypothesis on an apriori basis is not science but philosophy.
Here is a paper where Jeffrey’s summarizes some of his more recent work.
Doesn’t sound like any big breakthroughs yet.
Comment by JOHN_A_DESIGNER — March 9, 2011 @ 8:31 pm
March 9th, 2011 at 10:24 pm
Nick wrote:
You're talking 2 generations. How many generations of cave fish are we talking about here? According to Darwinian evolution, a hell of lot more than 2. And yet they're still able to interbreed with the sighted fish population they've supposedly been isolated from, which throws a big monkeywrench into the idea of Darwinian speciation.
How many epicycles do we need to compensate for before we discard this biological analog of geocentrism?
You're correct of course, but I'm a layman and I couldn't think of a better description of what the genes were doing than "convergence", especially when one of the papers in the article used the word "convergence" and KC described its opposite as "divergence".
Not that what's described as evolutionary convergence makes Neo-Darwinism look any better.
That's the great thing about standard evolutionary frameworks. You can make anything fit in them. Just like anybody could fit in Procrustes' bed.
Nobody said that the restoration of vision in cave fish was a prediction of the Theory of Evolution. Except maybe in someone's imagination.
Comment by angryoldfatman — March 9, 2011 @ 10:24 pm