The Appendix/Cave Fish Eyes/Etc. are (NOT) vestigial


#101

It’s simple–scientists have the actual fossils. Many may be seen in museums.

Anyone with common sense would see that getting the job done in one pass is preferable.


#102

Don’t you understand that while the Intelligent Designer is very intelligent he completely lacks common sense?


(Matthew Pevarnik) #103

Because you reject common descent, you can never understand vestigial structures

The first thing that needs to be established is common descent and phylogenetic relationships. For example, the appendix paper looked at 30-40 papers that they cite under ‘timetree construction.’ This can be done from fossils as I’ve posted extensively about in the other thread on making such cladograms or it can be done from on the molecular side from genes, genomes, ERVs, etc. Given that you know better and have better explanations than every paper that’s ever been written on such topics and comparative relationships and reject common descent, then it’s no wonder that you reject all vestigial structures.

We misunderstood each other here :hugs:

So my problem with all that you just said is your main conclusion is that:

But that simply is not true! Ultimately all the cave fish that regained sight did so through hybridization. The cave fish themselves may show very tiny changes when exposed to light as larvae but never ever did they actually develop sight with ‘a few generations.’ If they could do this, it would certain take much more than a few as they would have to randomly reduce the expression of the protein that causes methylation of certain DNA sites.

The Conspiracy against the Truth nonsense

Yes I know. They claim that there is this crazy persecution against them. All pseudoscientific cranks, climate change deniers or alternative medicine junk claim the same thing. There’s this conspiracy against “the truth” and their voice is just getting silenced by big-pharma, big-science, NASA, the FDA, etc. But it never occurs to people who follow such that maybe the reason their ideas are not published is because they are actually wrong. Crazy.

Not an engineer!

No not an engineer! My arch nemeses as a physicist. I used to think we could be friends but now I am doubting that possibility! :sob:

Also, one of the silliest things I’ve come across regarding engineers is the so called Salem Hypothesis:


(Chris Falter) #104

Hi Ashwin,

You missed some critical details in Romero’s article. Below, for example, is Figure 7 showing 6 photographs of larvae from 3 different populations, raised in 2 different conditions (continuous total darkness vs. continuous bright light).

MexicanusLarvae

Please examine carefully the eyes of the troglomorph larva raised in light (bottom right). Those eyes are still vestigial. To achieve some degree of sight, a troglomorph population must have a genetic infusion from the epigean (surface-dwelling) variant. And that is precisely what your second quote from the article, referring to a hybridization event in La Cueva Chica, demonstrates:

this new morph was the result of introgressive hybridization—transfer of genes from one population to another via repeated crosses. The transfer probably started in 1940 with the invasion of the cave environment by epigean individuals.

As for the first quote referring to populations in Sótano del Caballo Moro …

Interestingly, genetic analysis revealed that the cave-dwelling eyed fish is closer to the blind fish than to the surface population. This finding suggests that the cave eyed fish were originally members of the cave population and reacquired eyes and pigmentation following the collapse of the cave ceiling and exposure to the light.

…you are not examining the underlying data. Did Romero state that the two populations in Sótano del Caballo Moro are genetically identical, and that the phenotype varies solely due to conditions? No–he stated that the are populations are genetically different. Romero offers no support for the suggestion that the reappearance of sight was purely driven by environmental conditions in the absence of genetic changes. In fact, later in the paper he cites a specific cross-breeding event in another cave (La Cueva Chica) which introduced sight throughout a population in the course of just 43 years. Such a cross-breeding event would certainly be a plausible explanation for what happened in Sótano del Caballo Moro:

  • Why is the light-dwelling/seeing population closer to the neighboring troglomorphs? Most of the DNA pool would have came from the cave-dwelling portion of the population.
  • Why can the light-dwelling population see? The vision-positive alleles were positively selected for in the lighted portion of the cave.

It is vitally important to read the details of the research in order to put quotations in the appropriate context.

Blessings,
Chris


(Chris Falter) #105

Hi Ashwin,

Thought you’d enjoy this picture of an Australian marsupial mole:

marsupialmole

Note the vestigial eyes.

Blessings,
Chris


#106

Sure looks like a part of the caecum to me.


#107

LOL!  


(Ashwin S) #108

Actually the paper Romero was referring to narrowed down on two possibilities for the cave fish in the lighted region developing eyes. One was hybridisation and the other was that the blind fish developed eyes.I dont want to discount the second possibility. However let us go with established facts that both of us can agree on -

  1. Some of the Hybrids of cave fish taken from different caves and allowed to mate are recorded to have sight.
  2. The sighted variant found on the surface waters is the same species as the blind variant.

The above facts tells us that the complete genome of this fish involves well developed Sight.
The cave fish is a truncated/defective version.
Now, if sometime in the future, the cavefish develop into a seperate species, you could claim that this new species has vestigial eyes.
However, the fact is that Species of blind cave world over have a sighted counterpart and cross breeding leads back to development of sight. A case of divergence into a new species is yet to be found.
All current evidence points to this phenomenon being similar to different morphologies being developed in dogs through breeding programmes.

One scenario how this selective breeding happened is as below -
Surface fish got washed into caves. Fish with sight all swam back towards the light and reached the surface.Blind fish couldn’t do that, leading to selective breeding. This is validated by the fact that the fish in different caves seem to be blind for different reasons… and cross breeding the blind fish leads to restoration of sight.
This also proves that the various blind cave fish in the different caves had different ancestors.

The eyes in this species is not vestigial.
@Chris_Falter @pevaquark

One issue i see is that you jump to conclusions too quickly. Pls engage with people’s arguments before dismissing them as crazy.They point to specific examples such as an editor of a paper loosing his Job for publishing ID friendly papers after peer review.His version of the events are below.
http://www.richardsternberg.com/smithsonian.php

The second part of the claim is that any paper openly arguing for ID wouldn’t mostly not get published.I think this is entirely feasible as i have seen many arguments from scientists (including testimony under oath) why ideas such as Intelligent Design does not come under the ambit of Science.

You are correct in saying we misunderstood each other.I dont have anything against speciation occuring through adaptations and so i don’t see it as impossible for novel phenotypes to arise or existing phenotypes to be lost.However i dont think the process happens mainly through Random mutations/natural selection. I think there is enough information in the genome to bring about this change. And specific environmental triggers cause regulatory mechanisms to switch on and off leading to loss/gain of traits with the genetic information already present in the organism. (So i also believe there are limits to this ability to adapt according to the information present.)
So things like the appendix being lost and gained… or the same loss or gain of function happening in same/similar environments across clades/families look like a programmed response to me.
hence my aversion to the term vestigial. i see teleology… and the term vestigial denies it.

I dont see why an engineer should be an arch nemesis of a Physicist.We give you guys worth by actually making useful stuff from your general vague theories… :slight_smile:
Then you guys can go around taking the credit for it by saying all the technology in the world is based on the discoveries of physics/chemistry etc.You should be immensely grateful to us for making your life meaningful!

As to the blog shard by you… the reason is simple. Engineers are realists. We continually have to prove our ideas in real life machines/trials and that keeps us grounded in reality.
We also need to be able to communicate/translate our ideas into drawings/flow charts etc which other people can understand and execute into real world products/processes. This makes it very difficult to hide circular logic behind special words. We need to clearly define what we know for certain ( and i am not talking about just statistical relevance) and what we don’t know and also what we can’t know. This generates a particular mindset that is averse to fairy tale explanations posing as reality…
As to more engineers being jihadists… well engineers apply their knowledge and act on their beliefs. The Scientist version of a Jihadi would be the crazy imams developing the theoretical basis of why its ok to blow people up.
To be frank the blog you shared is juvenile. read a little more quality stuff.

A designer who created all life would have a different perspective from that of an average human being. “common sense” changes even among human beings based on cultural change. And you are applying it to a totally different being.
This is a pathetic argument.


#109

It was a humorous reply made to beaglelady, who got the joke.

You, on the other hand, appear to be humorless.

BTW, I am also an engineer.

And on a serious note, I would expect an intelligent designer that is also a good engineer to not give a bipedal creature a spine designed for a quadrupedal creature thereby subjecting the bipedal to back pain among other problems. Even for a designer who created all life don’t you think this would qualify as common sense?

From Wikipedia

The problems noted in the Wikipedia article shouldn’t have been a problem if we were actually designed and not the result of evolution reusing the spine that was already present.


#110

Not to mention how our capacity for speaking made us vulnerable to choking. Or babies coming out near a sewage system?


(Matthew Pevarnik) #111

I suppose I should confess something to you. This is how I actually go about posting on these forums:
image

I can see why you think this could be the case. You saying this does make me realize something that I have a tendency to do. From your perspective all you see is me making a broad sweeping statement about the fact that there really is no conspiracy against anti-evolution creationism. What you don’t see is the thousands of hours I’ve spent previous to this being on both sides of the coin and landing somewhere in the middle.

The Sternberg Controversy? Oh dear, yes they celebrate his martyrdom even though there are many more reasons for his dismissal. Here’s a third party’s take on the issue:

The Meyer paper wasn’t even very good and had many unsupported claims and it seems that Sternberg really wasn’t the greatest coworker and not the best at his actual job at the Smithsonian. There are many interesting parts for me reading through Sternberg’s take once again, including all the “anonymous” reviewers the paper supposedly had. The whole thing is really quite shady even if I want to look at Sternberg’s actions in the best light. Here is a critique of the Meyer paper that it would have been subject to had it actually been sent to scientists in the most relevant fields:
https://pandasthumb.org/archives/2004/08/meyers-hopeless-1.html

The conclusion I’ve found is very true for most critics of modern science:

There is nothing wrong with challenging conventional wisdom – continuing challenge is a core feature of science. But challengers should at least be aware of, read, cite, and specifically rebut the actual data that supports conventional wisdom, not merely construct a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, knocking down strawmen, and tendentious interpretations. Unless and until the “intelligent design” movement does this, they are not seriously in the game. They’re not even playing the same sport.

A story from when I joined an Electrical Engineering group as a postdoc. I started working with one of the engineers there on his project while I waited for my stuff to come in. He was try to measure what are called DNA nanotubes passing through a small channel and had been collecting data for about six months. My first thought was ‘I wonder what one should expect to see from a theoretical standpoint.’ He got upset with me and said ‘stop wasting your time doing all these calculations, we just need to analyze the data.’ Lo and behold, I demonstrated that he was actually measuring junk as the tubes were being ripped apart by the electric force inside which corresponded well to the data he was measuring. Needless to say, he did apologize!

So it was entirely meant to be a joke. I don’t seriously believe or endorse Salem’s hypothesis and I hoped that that would have been clear. It seems @Bill_II also had one that didn’t go over so well either.


#112

Or the routing of the laryngeal nerve in a giraffe.


(Steve Schaffner) #113

Excellent piece.


(George Brooks) #114

@Ashwin_s (and @Chris_Falter):

In fact, with variants as different as the blind fish in the cave and the sighted-fish (belonging to the same species), the question of “common ancestry” is not mute at all. In fact, it proves that “common ancestry” has much more explanatory power than simply saying “God specially creates most life forms”!

Do you think God would intentionally use Special Creation to a species that was both sighted and non-sighted (even without eyes?)?

Or does that seem much more like something that God would arrange through common descent, using Natural Selection to help execute his plans for that fish?


(Ashwin S) #115

You didnt sound like you were somewhere in the middle. Your stand was fairly clear… these guys dont get published because their ideas (or they themselves are crazy)

The same third party that seems to think Engineers are more prone to become religious psychopaths?
Didnt bother to read it.

Usually if scientist object to a paper. They publish their objection in another paper…
Would love to read a peer reviewed rebuttal…

Not an ideal engineer or scientist for that matter…

You might have meant it as a joke… but the article was a bit offensive… and totally dum.
Bad taste.


(Ashwin S) #116

No one denies ancestry within a species… Its a proven fact… All animals have biological parents. grand parents etc… and they inherit genes from them. However, if you extrapolate this truth… then you would require every species to arise from one pair of males and females. Yet scientists refuse to do this. .And its fair to say that all extrapolations need not be true.

If an Ad infinitum extrpolation of this fact backwards into history need not be true even at an intra-species level… It definitely could be wrong at a cross species level…
This is faulty logic.


(Ashwin S) #117

Glad to now you are an engineer Bill.

Have you looked in to this claim and similar claims deeply?
What are the alternatives?
And what are the differences in the spinal structure of a human from a cat? (we cant walk on fours )
And lastly, how much of these problems are related to ageing?
One argument i can think of without getting too much into details is that these are problems normally associated with ageing and required for death.
If the purpose was not for us to live for ever… we would not see these things.If the designer wanted to create creatures that could perish… then we would.

I am certain this is not going to be a popular answer.

Edit: As an engineer, you must know that we don’t design anything to last forever… we have our common sense reasons… I believe the creator has reasons different from ours…


(Matthew Pevarnik) #118

Middle ground = evolutionary creationism or some variant of that word. Mountains of evidence for common descent/theory of evolution + my personal experiences and faith choice in God.

The Salem Hypothesis was obviously satirical. The website doesn’t actually believe that and if you still think that, I’m sorry.

That’s very sad. It was even an article that was spoken positively of by @glipsnort who doesn’t tend to waste his time here finding links to obvious satire like me- you can see some select publications of his here: https://www.sabetilab.org/stephen-schaffner/

I wish you would actually read it and stop believing that there is some kind of conspiracy against Sternberg (hint: there’s not yet he is purposefully portrayed as a martyr for the ‘truth.’).

I give up. I doubt that you would as Meyer’s article wasn’t even peer reviewed yet it’s seen as gospel truth for so many. It was clear that it ignored large bodies of evidence (despite supposedly being a ‘literature review’) and cherry picked a few ideas from other ID articles (that don’t even support his hypothesis) and books that weren’t peer reviewed. Meyer also has no relevant background in any of the fields required to write such a paper but yet his publication went through.

If you say so. Glad you are a perfect combination of both.


#119

Deep enough to believe them.

I would expect an intelligent design to come up with something better than what we have. He is after all supposedly the great and powerful designer.

I have had lower back pain since I was 17 so I know that is not related to ageing.

They aren’t. Good to know the Intelligent Designer puts in planned obsolesce. As if there aren’t enough other build in mechanisms that limit our age.

Edit to add: Some of your “defenses” are getting to be quite amusing if I say so myself.


(George Brooks) #120

@Ashwin_s, maybe your analysis would have the correct conclusions if it had correct premises. You are incorrect when you say “… then you would require every species to arise from one pair …”

Individuals do not “evolve” - - populations evolve. And there are only a handful of populations that evolved by means of a single novel individual.

[[ NOTE: some song bird populations have been started by individuals who developed a novel song that was rejected by most of that populations available mating companions, except by relatives or offspring of the individual with the novel song. By definition, this leads to a new population that is, de facto, reproductively incompatible with the original population; over time, this leads to separate evolutionary responses to the environment. Additionally, some plants and simple animals or protists) are able to create a new population in a single generation by means of a single mutation. ]]

This means there is not a single pair behind most speciation events; speciation occurs at the population level.

So, the only way to conclude otherwise is to suggest that God “poofed” some species into existence. The fact that the predecessors of many of Earth’s existing larger mammals (elephants, rhinos, giraffes, tigers, bears, etc.) do not appear in the fossil stacks until after “proto-” versions of these animals (smaller and/or uniquely anatomically similar to the existing kinds) is the evidence that the final versions were not “poofed” into existence.

Further, these proto-versions of modern forms do not appear in the fossil stacks until after even earlier models first appear. And, ultimately speaking, the fact that none of these larger versions appear until after the extinction of all dinosaurs above a certain size, is the most compelling of all evidences that evolution on Earth requires a sequence of populations. If God “poofed” all these animals into existence at the same time, then we would find rhinos drowned along with triceratops, and giant marine lizards drowned with proto-whales.

But we do not.