Not much can be written after you watch the two videos above…
It is pretty easy to understand for those who choose to understand that the theory of abiogenesis and the probability of life spontaneously self-assembling is just a science-fiction story to fill the void for those who need to believe in something other than the obvious…
If the living cell can’t be reassembled in a lab, what evidence is there that life spontaneously self-assembled other than in science-fiction stories?
Now, let’s listen to the excuses…
Hardly, ” No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing”. If that is a possibility to be considered then the most commmonly used explanation for that would be designer. Perhaps one which created an archetypal cell.
As for gender, a design explanation chain of causation eventually requires an uncaused cause. Many of those are referred to by the male designation.
If not a designer how did this archetypal cell come about?
From wiki:” Crystallization is a complex and extensively-studied field, because depending on the conditions, a single fluid can solidify into many different possible forms. It can form a single crystal, perhaps with various possible phases, stoichiometries, impurities, defects, and habits. Or, it can form a polycrystal, with various possibilities for the size, arrangement, orientation, and phase of its grains. The final form of the solid is determined by the conditions under which the fluid is being solidified, such as the chemistry of the fluid, the ambient pressure, the temperature, and the speed with which all these parameters are changing.”
Could you elaborate on the path of study of the cell that would be analogous to this process?
You may be able to describe these things in simple terms. This is fine if all you want to do is give a very general outline, but it is entirely inappropriate if you want to understand the reality.
Here are descriptions which give us a fuller picture of these things.
Skin is not just some permeable material equivalent to coffee filter paper. It is an ever changing, dynamic, interacting complex of living substance that has to be viewed in relation to the whole organism. And the same goes for nerves, muscles and any other body tissues.
Good point. They are part of nature, just not explainable in terms of physics and chemistry.
In the same way that you cannot give a meaningful description of a Shakespeare play by examining the letters of the alphabet.
This is reductionism taken to extreme.
John Harshman,
If they are extant why would you assume they are intermediate?
Is your claim here that the Cambrian animals did not have circulatory systems?
The paper concludes that there is not a clear genetic pathway from prokaryotic to eukaryotic cells. The nuclear pore complex is an example and spliceosome comparison is not mentioned.
Rumraket,
There are also structures that lack similarity like the nuclear pore complex and the spliceosome. How do you propose that these structures arose from a trial and error process?
This is true but it is not your claim. You are claiming that one arose from other through a purely material process. Evidence of similarity does not demonstrate a reproductive transition occurred.
No assumptions necessary. “Intermediate” just means “between two points”. For any organ, one can point to extant organisms in which that organ has a complexity somewhere between nothing at all and the state in a human being. Think of Darwin’s description of eyes, for example.
Some of them, certainly, just as many extant animals have no circulatory systems. Do you know nothing about biology?
So though you reject the methodology, you accept the conclusion, and from the absence of knowledge you conclude…what?
Look, I don’t know what “naturalistic explanations” even means, other than empirical explanation, and only used your terminology because you did (and with scare quotes). Empiricism isn’t reductionism, so it isn’t limited to chemistry and physics, or any such thing. Thus, I don’t see where there’s any difference in “level” involving any sort of “naturalism” or some purported “higher level” explanation.
Not really, because you have to consider systems, like the nervous system.
Actually, you’re very much going to have to consider chemistry and physics in order to tell about the actual people involved. Maybe one of them has bipolar disorder, in which case you’re going to have to think about brain chemistry.
For health and strength, well, there’s a host of chemistry involved in health, not to mention with the issues involved with performance-enhancing drugs.
You assert that. but never support it. Considering people involves explanations that subsume chemistry and physics into systems that operate according to chemistry and physics, but which may be considered without explicit reference to them.
Anyway, what you wrote certainly doesn’t get to why Szostak isn’t going to consider miracles and “higher realms,” let alone why he’d have no problem with explanations involving humans or humanoid beings in his causal realm. In science you don’t get to just make things up. You have a problem with this.
Glen Davidson
We have evidence that changing the brain chemistry can change both thoughts and emotions.
We have evidence that changing the structure of the brain can change both thoughts and emotions.
It seems at least at some level of explanation both thoughts and emotions can be explained thru chemistry and physics.
That analogy makes no sense to me. I understand that you think a materialist account at the level of atoms would lack something. What I’m missing is why you think so.
But nothing I said here should be particularly controversial. Again, I understand that you disagree. I just don’t see why. What is it about the boxing match you think would be missing in a total account at the level of atoms?
John Harshman,
I think the argument is how over less than 100M years can we build the sequences that account for the complexity of mobile Cambrian animals. The evidence shows they have circulatory systems which are irreducibly complex. i.e. remove a key component the animal dies.
This strongly suggests that the Cambrian animals were a separate origin event and brings the design argument to the forefront.
The paper shows that 2400 yeast (eukaryotic) genes do not have homologs in prokaryotic cells. Given that Venter has created a living cell with 473 genes the eukaryotic cell transition from a gene perspective is more daunting then OOL. This strongly suggests that the eukaryotic cell was a separate origin event.
Fortunately given the design argument that is a chip shot.
We really need to stop paying attention to these doofuses. Phoodoo Jmac and colewd in particular are simply hopeless PRATT spouting idiots.
What evidence do you have that any Cambrian animals had circulatory systems at all, let alone that they’re irreducibly complex?
Separate origin event from what? And how do you manage to ignore the evidence for gradual origin of Cambrian animals as set forth in my post you claim to have read?
Separate from what? And are you aware that animals are eukaryotes, so if animals are “a separate origin event”, doesn’t that make eukaryotes at least two separate origin events? You need to get your story straight.
Also, when you say “prokaryotic cells” are you referring just to eubacteria or to archaeans too? Are you aware of the several recently discovered major groups of archaeans? What do you know about their genomes?
Yes, anything is a chip shot if you allow for poofing of anything from nothing at any time. But I don’t see the science in it. And I don’t see that as fortunate; I see it as a weakness of the design “argument”.
You understand that the description you quoted was of human skin, specifically, right? We were talking about Cambrian animals. “Has to be viewed in relation to the whole organism” is a charming and meaningless buzzphrase whose entire purpose is to prevent thought. And you have managed to change the subject from the evolution of respiratory systems to the evolution of skin. I suppose you can push that regression back quite a ways, but does it help the claim that respiratory systems are too complex to have evolved naturally? I don’t think so.
Whatever you meant here will do.
What direction does that “another direction” point?
John Harshman,
Because the size range of the Cambrian animals are too large from 3mm to 70cm. Per fb.com
So at what point did the circulatory system appear? It looks like probably fairly early in the Cambrian where we have evidence of larger Trilobites. This link shows Trilobite size variation across the Cambrian and beyond.
http://www.trilobites.us/figures/figimages/trilobite-length-variation-sensu-bell.jpg
On what basis do you think you can show evidence of gradual increase in complexity?
100 different types of archaean DNA were part of Koonin’s comparison.
A reasonable criticism but I think the idea of design in biology can lead to interesting exploration. If I explore the cell with the idea it is filled with design concepts the big picture may look very different.
That still puts them ahead of Mung, and Joe G’s socks.
Excellent. You have finally given me some data and a real argument for something. I believe that’s a milestone. Yes, you have provided evidence that some Cambrian animals had moderately complex circulatory systems (though none at all as complex as a modern gnathostome’s). But note that it’s the gradual increase in size that is the impetus, which allows for gradual expansion from no circulatory system (small animal) through various stages to a complex one (large animal).
You showed some yourself in the gradual size increase. Now of course most of this happened before the fossil record of trilobites, which begins toward the end of the Early Cambrian. And we have a much less satisfactory fossil record for those times. We do however have the Ediacaran fauna, gradual increase in number and sizes of burrows and tracks throughout the latest Ediacaran, the small, shelly assemblage of the first two Cambrian stages, and of course the wide and fairly continuous variation in complexity of circulation among extant species.
Yes, I see they were. But some of those were discovered only in the past few years. Who’s to say there aren’t more waiting? And each new discovery has provided more homologous genes. This is to be expected given reasonable rates of gene loss and origination in various lineages. More sampling tends to find more homology and drive those homologies deeper into the tree.
So why do you reject all the conclusions of the paper and focus only on one number?
Fine words, but that doesn’t seem to be the case so far. No insights whatsoever have come from ID. In you, it serves only to obscure.
John is just being silly again.
See: The Evolution of Organ Systems
For instance, why the gradual progression of complexity in life forms?This would seem to be a choice.
How does one create populations with new designs?
The originator of the designs would be much further advanced than humans. Would such an advanced intelligence be comprehensible to our relatively primitive minds?
Is the Earth designed? How would one test the hypothesis?
The idea that life was designed has been around for thousands of years. Why do you suppose that nothing like you describe has ever happened?
Great, you can link an entire book. What are we supposed to glean from this?
So none of this is evidence that molecular evolution occurred outwith a cell membrane.
I agree it isn’t and never claimed otherwise.
Every cell consists of a concentration of dynamic physical activity. If there was a possibility of tracking the history of each molecule within a cell at any one time we would see that these molecules were previously scattered widely throughout the wider world and they will disperse again over the future life of the cell and beyond.
Physical substance comes and goes but the cell retains its continuity. The essence of the cell is in its continuity over time .not in the material that is present at some particular time. The archetype is not some external nebulous entity hovering over the living form. It is the living being seen not from a spacial perspective but seen from a time perspective.
That’s all fine and good, but that doesn’t give us any reasons to reject physicalism in ontology or empiricism in epistemology.
What you would need here is an argument as to why forms or structures enabate from a “spiritual” realm to a “physical” one, rather than understanding forms or structures as purely imnanent to the natural world.
In other words, simply calling attention to the fact that life involves self-perpetuating structures doesn’t establish a Neoplatonic account of those structures, esp in light of the Aristotelian alternative.
Like the ship of Theseus.
Glen Davidson
You are not understanding what it means to practice “Goethean Science”. It is not done by philosophising about nature but by experiencing nature. As soon as we go beyond experience to speculate about what we understand by the terms spiritual, natural or the like we have departed from Goethe’s method.
I would not call the archetype spiritual but rather supersensible in the sense that we have to go beyond what we think of as our normal senses to experience it. We should use our senses to examine the subject, say a plant in all its modes of existence, all of its expressions of shapes, colours, nature of growth and everything else. We then hold all of this in our mind and let the images we have experienced merge into each other in a panoramic view of the plant in its existence from seed to death, in growth and decay.
By using our minds in this way we can have a higher experience within experience which does not go beyond reality to some “spiritual realm” that we have speculated to exist. We most definitely need to stay within experience. So I cannot persuade anyone to experience these things just as I could not persuade a blind person to see colours.
There is nothing wrong with speculation so long as we recognise it for what it is.
CharlieM,
I don’t think there’s anything supersensible about our experience of form or organic unity. On the contrary: I think we experience structures, forms, unities precisely through sensible encounters with them.
If one insists on starting off with atomic, isolated sensations as building-blocks of experience, then yes, there does need to be Something Else to play a unifying, structuring role. But if one does not accept that view of sensations, then there’s no need for the Something Else.
As long as the analogy isn’t taken too far. The ship of Theseus is built from without following a static design. Living entities are dynamic forms developed from within.
There are drugs…
Glen Davidson
OMagain,
I think it is happening. If you google biological design and system biology you can see some of the work here.
newton,
Interesting question. Maybe a good subject for an op.
Would it be a good use of resources? Without knowing the abilities and goals of an unknown designer would the speculation of design be useful?
John Harshman,
I agree with all your points here but it does not explain transition from early multicellular organisms (sponges) to the complex systems of the Trilobites.
A single component of this system like a heart is useless without all the other parts of the system.
These are integrated systems which require differentiated cells, a process that needs to be part of embryo development. Where does the genetic information come from to build these complex animals? Where did hox genes enter into the picture? Where did the genetic information come from that codes for these genes?
The conclusion of this paper is like most papers on evolution which assumes universal common descent as a working hypothesis. Since I am skeptical of this hypothesis I don’t automatically accept the conclusion which is based on this assumption.
I do not focus on one number but look at the raw data as evidence.
In this case the raw data is contrary to the UCD assumption. You will claim that there is possibly missing data but that claim is based on the UCD assumption.
The data itself goes against a materialistic conclusion for the origin of the eukaryotic cell.
What use is half an eye? Or a quarter of an ear?
You are good at noting this. You’ve done it several times now. You can stop.
Simply say what the data itself points towards instead of saying what it points away from.
That would be relevant if evolution was about “putting components together” but that’s not how it works. Life is not a fucking jigsaw puzzle. It should be obvious to anyone with any meaningful education, that’s certainly not you.
For the emptienth time, how does an embryo get by if “a heart is useless without all the other parts”? I mean, seriously. Stop it
You know nothing about “the complex systems of the trilobites” other than that they couldn’t have relied on simple diffusion. (Sponges, incidentally, have something that could be called a respiratory system, as they are constantly drawing currents of water through their bodies.) It’s all the intermediate conditions we can see in extant species that explain the transition simply by showing that intermediate steps can exist.
Now, when you say that a heart is useless without all the other parts, just what parts are you talking about? What do you know about circulation in arthropods? I think you know nothing.
Sponges are integrated systems, have differentiated cells, and embryo development too, you know. Or most likely you don’t. The genetic information is mostly inherited from prior organisms, with occasional duplication and divergence, re-purposing, or recruitment of previously non-functional sequences. It’s just the sort of thing that goes on today.
As for Hox genes, they came from prior, similar genes. Sponges have Hox homologs, though the actual Hox genes seem to have arisen in the metazoan ancestor. Jellyfish have Hox genes.
You’ve never seen any raw data in your life and wouldn’t recognize it if you did. And it doesn’t take any assumption of UCD to be able to tell that genes arise and are lost throughout life.
But since we’re on the Cambrian explosion, why don’t you explain what you think happened? Was it a big creation event? And if so, does that mean that all extant animals descend from Cambrian animals, or were there lots and lots of subsequent creation events?
Below is an image from Form and Cause in Goethe’s Morphology by Ronald Brady. This depicts a succession of leaves from a single buttercup plant in the order that they appear moving clockwise from lower left to lower right. The order of the different shapes make it very easy to picture in the imagination each form morphing from the previous form, in other words each form developing out of the previous form. But this is not the case, each form is not caused by a modification of the previous form. Each are particularised instances of a general form. We recognise the similarity of form but this is not due to common descent. During the growth of the plant one form of leaf follows the other but their similarity is not caused by the former developing out of the latter, it is caused by them both being a manifestation of an underlying unity.
As Brady says:
and further:
So showing the intermediate steps can exist does not, of necessity, show that the configuration of the former in the series is the cause of the configuration of the latter. There are other explanations, as demonstrated in the case of buttercup leaves.
Here is another interesting excerpt from the link which is worth pondering:
In Goethe’s thinking, idea is as much a part of the object under study as is its physical appearance to the senses. And I agree with this.
oops. Forgot to add the image.
Quite true, stripped of the meaningless mysticism. The point of intermediate forms is to show that transformations are plausible, though Bill claims they are not. It’s the nested hierarchy of life and its fit to the fossil record that show descent, hence transformation.
I have no idea what that means, so can’t agree or disagree.
John Harshman,
I understand that Arthropods have open circulatory systems (we have a closed system containing veins and arteries). It still does not change the claim that a heart on its own does not help the animal. It requires a cavity for the fluid, it requires a fluid that contains proteins that can transport both oxygen and co2.
Interesting thanks.
Why don’t you think I have never seen raw data? I guess data consolidated in a chart is not raw?
The question is not that genes come and go it is how they come and go.
Until we have a mechanism that can move from functional DNA of animal A to functional DNA of animal B where new genes and capabilities are formed then it looks like a creation event.
You made a good point about different ways that multicellular animals receive oxygen. I would say that each of these systems would need a unique creation event whatever specifically that means.
What do you mean “arthropod”? Isn’t that some kind of artificial category imagined by biologists based on simple similarity? How do you know that trilobites shared any of the characters generally associated with arthropods other than having jointed legs? Inferences about unpreserved anatomy require assumptions of phylogeny, which you reject. Just about every animal has spaces in between tissues, even though without hearts, so that’s not a problem. Proteins that transport oxygen and CO2 are not necessary. Many animals do without them. And the primary function of hemolymph in most arthropods is not gas transport anyway.
That’s what you say when a claim of yours is refuted and you can’t think of any other response.
Is that what you were talking about? But you denied basing your conclusion on one number. Anyway, no, that isn’t raw data. The raw data would be the surveys of genomes. But I was really commenting on your inability to get very far into anything you read; you only look for nuggets you can use to support your preconceptions.
That’s fairly well known. There are a number of ways for each. But no, that isn’t the question. The question is whether the data support separate creation of animals, or some groups of animals, or whatever. You have never set out what you think happens. I suppose that’s wise, since any hypothesis you would be likely to advance wouldn’t fit the data, and making yourself explicit would expose the vacuity of your thinking.
What looks like a creation event? What new genes? (I think I’ve dealt with the capabilities.) Again, you are too vague to address. What do you think happened in the Cambrian explosion?
Yes, you would say that. But what argument do you have for your belief? And how many unique creation events are you proposing, what are they and what does “whatever specifically that means” even refer to?
John Harshman,
The real issue here is how new capabilities are created. I do reject that a mechanism that starts with a random change and is directed by advantage can create these new features.
It is rare that animals can live without oxygen carrying proteins here per wiki are the proteins for invertebrates.
Here is an example of a fish and environment where an oxygen carrying protein is not required. Note that the conditions are very cold and the fish has lots of veins and arteries. The claim here is that the efficiency is 10% of a system with an oxygen transporting protein.
The argument is that these complex features that we see require complex DNA sequences. Random change to a DNA sequence is much more likely to break it down then it is to find function. When Rumraket argued against Doug Axe’s claims his best experiment still had 1 million more ways that a protein would not find function then it would locate a function for a short peptide sequence. The spliceosome has greater then 200 proteins and probably takes 300k nucleotides to build. How many proteins does it take to build and operate a human circulatory system?
The sequential nature of DNA is evidence of creation. A new animal with new features like a vein and artery based circulation system requires a mind to develop the sequential information to build the animal.
I am having to find nuggets inside papers that are built from preconceptions. The fact that I can find nuggets at all is very interesting.
John Harshman,
More of evidence of oxygen transport proteins in Trilobites. https://doi.org/10.2110/palo.2014.073
Yes, but not in the way you think. It’s called cherry-picking, and it’s about your psychology more than it’s about actual data.
Some arthropods have hemocyanins, most do not. Cherry-picking again. Hemoglobin, of course, is part of an ancient family of proteins that long precede circulatory systems. Why, in your very own body you have myoglobins, which have nothing to do with circulation.
Ah, but do they require new complex DNA sequences? And you still seem to have no idea how natural selection works. Even if most mutations are deleterious, it’s the rare beneficial ones that selection makes more of. Your personal incredulity counts for nothing, and certainly can’t outweigh the plentiful evidence of phylogeny.
Sorry, no cigar. Marella splendens isn’t a trilobite, and it would require a phylogenetic hypothesis, which you reject, to make it relevant to trilobites. Good paper, though.
I’ve asked you a great many times to tell me what you think happened in the Cambrian explosion, and you have always ignored the request. Why?
Indeed, so you keep saying. But apart from an expression of personal incredulity, no arguments have been forthcoming for this claim. And personal incredulity has no epistemic significance.
Heh, no. Actually the paper that reported the greatest success rate found that 4 out of 8 tested proteins had the desired function. (I mistakenly say it’s 1 in 4, when it’s half of the proteins tested). Which is quite an astonishing result and I would agree that can’t be representative for all functions in all of protein sequence space. It does imply, though, that most functions probably exist abundantly but at very low levels of activity.
There were several others with success rates of 1 in 1000 and 1 in a few hundred.
These numbers are orders of magnitude higher than what you say the “highest” reported number was in my post. In any case, this indicates that some functions are truly abundant in protein sequence space. Which implies it is often times simply a matter of selection to enhance these latent functions should they be found advantageous.
Even so, a success rate of 1 in a million is 71 orders of magnitude more frequent that Axe’s ex recto assertion.
The same amount as a chimpanzee circulatory system.