- Despite lack of observational basis, Darwin proposed Universal Common Descent (UCD) saying: “Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed“. He also said elsewhere (referring to UCD): “…the littlest creature (or four or five of them)…” With his remarks, Darwin left the door open to creation (“life was first breathed”), but since then, Neo-Darwinists have rejected creation and replaced it with belief in undirected abiogenesis while maintaining belief in UCD.
- UCD is incompatible with the current view of Earth as just an ordinary planet circling an ordinary star located nowhere special inside an ordinary galaxy. If Earth is “nothing special” and abiogenesis is an ordinary “arising” of life from non-living matter, spontaneous abiogenesis would be a trivial common occurrence here on Earth as well as throughout the Universe, and we would have many “trees of life” instead of one. However, until now, all abiogenesis experiments have failed to produce life, spontaneous generation has been rejected, and the Fermi paradox stands, all these keeping the single “tree of life” and UCD hypothesis still alive and still inexplicable.
- Conditions for starting life should be similar to those required for sustaining it. The Big Bang model mandates a beginning of life. Furthermore, once started life must be sustained by the same or very similar environment. And since life is being sustained now on Earth, abiogenesis should be ongoing contrary to all observations to date. Tidal pools, deep sea hydrothermal vents, and the undersurface of ice caps have been hypothesized to originate abiogenesis due to their persistent energy gradients, but no abiogenesis or its intermediate phases have been observed around these sites. Given these, the only methodological naturalistic alternative is ‘limited window of opportunity for abiogenesis which suggests primordial life substantially different than all known forms of life, and perhaps originating on another planet followed by panspermia. However, this alternative defies Occam’s razor and the absence of supporting evidence including the earliest ever known fossils (stromatolites) that are of commonly occurring cyanobacteria rather than of alien origin.
- Universal Common Descent requires an inexplicable biologic singularity. All known forms of life are based on the same fundamental biochemical organization, so either abiogenesis happened only once or it happened freely for a while but then it stopped when the ‘window of opportunity’ closed and only one organism survived to become the Last Universal Common Ancestor (LUCA) of all existing life on Earth. However, these two biologic singularities should be unacceptable given the lack of evidence and the assumption of continuity in nature. Furthermore, the second scenario requires two discontinuities: one for the cessation of abiogenesis and the second one for the bottleneck leading to LUCA.
- In conclusion, UCD hypothesis leads to a number of bad and very bad scenarios: a) Earth is “nothing special” should lead to a “forest of life” rather than a single “tree of life” and to ubiquitous abiogenesis (unobserved); b) Alien life plus panspermia is refuted by the Fermi paradox and oldest known stromatolites fossils; c) Single event abiogenesis is an unsupported and therefore unacceptable singularity; d) ‘Window of opportunity’ abiogenesis followed by LUCA bottleneck is even less acceptable double-singularity. And this brings us back to Darwin’s “open door” to creation, perhaps the most rational alternative that fits all biologic observations.
Pro-Con Notes
Con: Maybe abiogenesis is happening a lot. I think the already existing life would dispose of it quickly though.
Pro: if so, 1. We should be able to duplicate abiogenesis in the lab; 2. We should see at least some of the intermediate abiogenesis steps in nature; 3. Existing life can only process what looks like food. Cellulose is a well known organic material that cannot be broken down by a lot of organisms and is known to last as very long time in dry conditions.
What? Why didn’t I say that in the first place?
Gee, how did I enter this conversation?
To which you replied:
Like I said, ‘A simple, “Gee, I didn’t think that through” would suffice.’
So my apologies for accusing you of a cover-up. I mistakenly assumed that you were smart enough to follow along in a conversation that you were having.
It won’t happen again.
You would have to love the irony though if information theory could be used to support common descent!
It was an interesting proposal. I will keep it in mind and see if I can come up with anything that makes sense from information theory with ancestor as source and descendant as receiver and the intervening path as a communications channel where we can try to recover the signal from the source at the output of the channel.
It was a sincere cool idea from me to you!
Claim retracted.
But speaking of keeping track of a conversation, it is THIS comment of yours that I have been responding to and that I have been disputing (wasn’t that obvious?):
I mistakenly assumed that you were smart enough to follow along in a conversation that you were having. It probably will happen again. Ta.
Good grief.
phoodoo:
John:
Pretty clear that we are talking about processes here, mechanisms.
Mung snark:
Allan
Mung snark:
John snark:
Mung snark:
Later Mung:
Which Mung has conceded was in error. I mean, it’s a rather obvious category error, and it is Mung’s, not John’s.
I entered the conversation to point out this error.
John was discussing processes, mechanisms by which gene regulation is modified. Mung wanted to talk about competing schools of thought in evolutionary theory, but he crashed the Segway.
There’s some unlinked context over at PS that shows that Mung has not completely lost the plot. Apparently.
Significance in what sense?
Evolutionary head propagandist? HGT facilitates evolution. Why would anybody who actually understand evolution want to deny HGT?
I’m still lost. You talk as if HGT was something that went against evolution, when it clearly is a phenomenon that makes it much easier for it to happen.
Again, why would anybody deflect? HGT is an interesting mechanism in the evolutionary repertoire.
Oh! I see! You’re projecting from your religious inclinations and you think that unless it’s some mechanism proposed by Darwin then it’s not evolution. Right? Well phoodoo, you’ve got that very wrong. It’s not about worshipping some figure, even someone as important as Darwin in the development of evolutionary theory. It’s about getting better and better understanding about how things happen.
Some more projection on your part here phoodoo.
Enough to notice that you have no idea. You know that HGT is a natural phenomenon, right? That nobody has caught some magical being in the sky puffing genes into existence and then, for example, building them into antibiotic resistance “cassettes” that this being then inserts into all sorts of microbes. That what they catch in the act are plasmids, viruses. You know this, right?
Did I call it or what? A totally irrelevant objection. The conversation at Peaceful Science has nothing to do with your present misunderstanding.
As it happens, there isn’t. All it shows is that Mung never had the plot.
So if you were “performing ID-math(tm)”, can you give us the figures you were using?
Dpp is “capable of rapid diffusion in all directions, and yet gradients form slower, directionally and independent of morphogen production rates.”
From the article by Jessica L. Erickson, where I took the above quote from:
To say that “Dpp copy number results in embryonic cells assuming more dorsal fates” is a very misleading statement.
More from the article
There are several coordinated factors which contribute to the directions of growth and thus the morphology of the individual organism. Every stage of development expresses the archetype in its own unique way. And the correct growth is achieved by maintaining the appropriate balance between production and destruction of proteins such as Dpp.
And this is an enduring feature of all living systems from the molecular scale to earthly life as a whole, it is sustained by maintaining the balance between growth and decay, life and death. Blind evolution would not take this maintenance of balance over time into account because it has no thought for the future and balance can only be maintained by anticipating the future before it happens.
What is wrong with saying that individual cells evolve during the development of a multi-cellular organism?
A heat seeking missile is aiming for the source of heat but we do not say that it has the intention to hit its target. The latter has more of an implication of consciousness than the former.
You do have a point in that we should not jump to conclusions without evidence.
But we do witness aspects of nature where structures are in place in readiness for future use. Eyes before sight, lungs before air breathing, birds nests before eggs and so on.
End-Directed. Directed towards an end. It makes no claim about whether the directedness or the end are natural or not.
They maybe anomalous with respect to eukaryotes, but are they anomalous in prokaryotes? I would say that its common appearance here makes the species concept that is quite apt for metazoan redundant when it is applied to prokaryotes.
And I have no problem with agreeing that common descent is a well established feature within eukaryotes. Just how linear and extensive it is I am not so sure.
The commonality of genes between widely differing species tells me that it is the way genes are organised and not the genes themselves that make the difference.
I would say our difference of opinion lies in the way we see this organising principle.
They are right there in the comment I linked to originally.
No, it is not. I even quoted from the review that you cited regarding the effect of injecting Dpp transcripts into the embryo.
The fact that CharlieM is capable of mindlessly cutting&pasting from yet another article about imaginal wing development is entirely irrelevant to embryonic pattern formation. You are doing it again, and it makes you appear unaware that drosophila pupate…
If your comment included an attempt to explain why injecting transcripts into embryos leads to more dorsal ectodermal fates, I must have missed it. Could you be more specific?
Impenetrability, that’s what I say.
I did not say that it cannot be transferred in this way, I said it need not be.
Let’s review:
John is clearly saying that neutral theory is to random genetic drift as poodles are to dogs.
I am rather clearly talking about the neutral theory of evolution.
John reiterates his earlier claim. He certainly appears to be disagreeing with my statement that neutral theory is not the same as random genetic drift.
Even Joe picked up on the fact that I was talking about neutral theory. He probably read what I actually wrote and even understood the reference to 1968.
John essentially admits he hasn’t been following along all that well and still seems clueless that I am talking about neutral theory, in spite of the repeated mentions and references, and then accuses me of making a claim i never made.
DNA_Jock, for whatever reason, turns a blind eye.
It was only after this that I made my comment that sparked off this whole series of exchanges with DNA_Jock. It doesn’t make my comment right or appropriate, I apologized and retracted it, but DNA_Jock needs to consider the importance of context and no be so quick to castigate people for misbehavior.
And you should have left it at that rather than also accusing me of an attempted cover-up followed up by what are very much in essence accusations of lying about whether or not there was an attempted cover-up.
As you saw, once you pointed that statement about John out to me (admittedly for the second time) I promptly addressed it.
Your “pointing out this error” was obscured by your other baseless allegations. Keep that in mind for the future.
Naah, Mung; originally, I only pointed out that you appeared to be trying to cover up your error. A friendly ‘fix this’ heads-up. You promptly doubled down, which provided a basis…
Yes, John was slow to pick up on your segue from processes (the original topic of the conversation, including your original “Neutral evolution” comment) to schools of evolutionary thought, because it was a total non-sequitur on your part.
John is clearly aware that you don’t always use the correct words to describe what you mean, and is making allowances, assuming that you have not just changed the subject from neutral evolution.
I’m not sure you know what “neutral theory” is; you seem to be confusing it with “the neutral theory”. And confusing both with “neutral evolution”, which was your original statement. I tried to make the differences clear, but you seem to have ignored that. Now of course neutral theory (the mathematical population genetics of neutral evolutiion) is not the same as genetic drift; mathematics is not the same as a phenomenon. But it hardly seems necessary for anyone to say that, and I don’t believe that’s what you were trying to say.
You changed the subject. Perhaps you didn’t notice. You started with neutral evolution and changed to neutral theory, by which you possibly mean the neutral theory. Hard to tell what you mean, because there’s always the suspicion that you don’t know what you’re saying.
No, John admits that you aren’t very good at expressing yourself. I think that’s compounded by your desperate attempts to disguise a simple initial error.
Click the link boys. Then follow the instructions.
neutral evolution
Please explain what you mean. Please explain why you were not wrong to say that I had left out neutral evolution from a list of evolutionary processes when I did mention drift.
So what’s the deal with this “directed evolution” oxymoron?
http://nonlin.org/chemistry-nobel-2018/
Wasn’t the whole point of “evolution” to separate creation from creator? And now they let the intelligent agent back in? I would not be a happy evolutionist with this interpretation.
In this case, not only are “random mutations” not entirely random as the mutations desired had to converge towards a clear, specified target, but also “natural selection” has been replaced by Intelligent Selection clearly done by qualified researches pursuing a specific goal. At best this would be called “artificial selection”, but even that is misleading since organism breeding is a human activity that goes well beyond simple ‘selection’.
The process used is simple organism breeding as done by mankind for thousands of years, in this case sped up by advanced technologies.
If “evolution” needs “directions”, then IDsts and neo-Darwinists are all a big, happy, continuously quarreling family 🙂
Anomalous means anomalous, regardless what group we are talking about. The point I am trying to get you to grasp is that an anomaly is an anomaly because it goes against the expectation of simple vertical descent. That is, there must be a pattern of vertical descent in the first place against which such deviations stand out. What you are proposing is classically Creationist: to say that because there are anomalies, everything could be ‘anomalous’, and there is no such thing as pattern.
You almost seem to wish to use the things that can only be discovered by phylogenetic analysis to be an argument against the very techniques of phylogenetic analysis, which is, if you did but know it, quite a paradoxical position to espouse.
No one mentioned species till you, just now. It’s true, species concepts do not apply well across the boundary. The reason is recombinant sex, but it’s not the reason there is more gene transfer observed in prokaryote lineages. And don’t forget what we were talking about: the relationship of mitochondria to prokaryotes.
Well, what does the evidence say? If gene transfer is comparatively rare, and the signal of common descent comparatively strong, what’s the issue? I mean, these are the organisms people particularly agonise over. Especially chimps …
Is the hierarchic structure of gene relationships at close taxonomic removes not also represented at higher levels? Where does the boundary reside, where sequence commonality stops representing common descent and starts representing some mysterious Other?
Well, you were rather dismissive of gene transfer a few posts back, some kind of feeble attempt by Darwinists to keep things ‘blind’. But here’s a phenomenon with some very suggestive characteristics. What would lead us to reject the possibility that the mitochondrion started out as an intracellular parasite, like Wolbachia? Don’t forget, phylogenetic analysis places it in the alpha proteobacteria.
So what was Entropy trying to convey when he told me that cell fifferentiation was controlled by the products of a couple of “master” genes? He did not specify which genes exactly.
He just directed me to this link and I have included this quote from it:
From the same web page it tells us:
The page also lists well over a hundred homeobox genes spread over at least four chromosomes in humans.
Which pair of “master” genes do you think he was he talking about?
So the development of the fertilised egg is turning out to be much more complicated than it just being kicked off by a couple of master genes.
From this article, “The maternal-to-zygotic transition during vertebrate development: a model for reprogramming”.
So complex regulation is in evidence from the very beginning of fertilisation.
They continue:
Such organisation cannot come from a point within the system. The control comes from above, from the organism as a whole, which to begin with is a single cell. The organism takes account of all the internal and external signals it receives and it acts accordingly. And this is still happening in each of us as multi-cellular organisms. Our bodies stabilise themselves through homeostasis. And the most fundamental aspect of achieving this is by coordinating the appropriate gene expressions. Genes are expressed on signals coming from the body. During exercise genetic activity activates the production of the appropriate substances and signals to increase our heart rate, produce sweat and so on.
“Master” control comes from above the genes, not within the genes.
1. See my replies to Allan above.
2. Name those genes.
Here is very thought provoking, informative short video by Denis Noble. In it he explains the limits of mathematical models and why this rules out a belief that biology is just the application of physics and chemistry..
He formulated the principle of biological relativity which states that there is no privileged level level of causation in biological systems.
He says:
He concludes that the central dogma should “never have been used to back up the general theory of evolutionary biology”.
CharlieM,
I think questions about other people’s posts are best directed at them. Still, there is no conflict between the initiation of a long cascade of ‘downstream’ consequences – eg SRY in mammalian gender differentiation – and my statement that the molecular biology responsible for given phenotypic alleles may be due to regulatory differences rather than differences in exons.
CharlieM,
Well, good for Noble. Shall I don the glove puppet of someone who thinks otherwise, and we can have a play-fight via the words of others?
CharlieM,
Maybe, but the source of the original transcript of a given RNA polymerase molecule has little to do with that.
Yes. For those who only accept common descent within created kinds questions like this expose that their acceptance of common descent within created kinds is a priori and not at all based on the evidence for common descent that scientists depend on.
If I had an answer to that question I might not accept universal common descent. Until then …
I don’t deny that there are similar genes in unrelated species. What I would not want to do is to assume that they got there by a certain evolutionary pathway just because that pathway strengthened my prior belief in how I think evolution should work.
I believe that HGT is a process which is common and natural to organisms such as bacteria. Genetic recombination is achieved in bacteria by way of HGT, and genetic recombination is achieved in diploid eukariotes by way of meiosis. This is consistent with my thinking that, not individual bacteria, but groups of bacteria at a higher taxonomic level should be treated as equivalent to individual higher animals. In higher animals individuals are made up of a community of cells concentrated in space, in bacteria individuals are diffused in space. Slime molds are examples of an intermediate level.
By “blind” I mean acting in a way that takes no account of the future. Bacterial conjugation is not blind in that it is a purposeful process which allows genetic material to be transferred between bacteria. And bacteria have the ability to also pick up DNA freely from their environment. Once inside the bacteria, the DNA will be used by the cell as appropriate.
We could compare sequences in as many genomes as possible and think about how plausible it would be for homologous sequences to show up in the organisms that they are found in. With the ever expanding amount of data that is becoming available, researchers are finding more and more sequences which are “out of position” in phylogenic trees. (See the example I have provided below).
There is evidence. For example, the frequency of convergent evolution points to a higher level of organisation.
Yes, and testing is difficult in a historical science such as in the study of the evolution of life. A person’s philosophical viewpoint has a great deal of influence on what they are willing to accept as a likely scenario.
Save them from the evidence which conflicts with the neat branching tree which I suspect most early evolutionists would have wished for. It has been found to be quite messy and this has to be accounted for by the means of blind evolutionary forces, hence “mistakes” in genomes due to extranious DNA insertions transferred horizontally.
If intelligence is involved there does not need to be a physical transfer mechanism.
As I said, I believe that HGT is a natural process in prokaryotes.
What mechanism? There does not have to be a mechanism.
Again, there does not have to be a transfer mechanism.
DNA Jumps Between Vertebrates
So this stretch of DNA can be found in many animals including elephants, horses, platypuses, pythons, sea snakes, geckos, sea urchins, zebrafish and ticks. This is what I mean by using HGT to save the theory.
Of course it is. An individual termite has a certain level of organisation. A termite nest has a certain level of organisation. The whole system includes the organisation of the individual termites, it also includes the organisation of the termite nest. The termite can be seen as one level of organisation, the nest can be seen as one level of organisation, the whole can be seen as two levels of organisation. Two is a higher number than one.
The sending bacterium has no idea how the DNA will affect the recieving bacterium, and vice versa. That’s the sense in which it is blind. Interestingly bacteria a tendency to expel foreign DNA that turns out to be of no immediate benefit. It is a well-known phenomenon that bacteria will, for example, lose plasmids if they are not under selective pressure to keep them. That’s why when you transform bacteria with plasmids in the lab, the plasmids are usually designed with that in mind so they carry an antibiotic resistance gene, and then you grow the bacteria in the relevant antibiotic such that the bacteria are under selective pressure to keep the plasmid and copy it when they divide.
And yet there is an immediate and obvious mechanism by which that can happen, the ticks. What you call “save the theory” as if that is somehow an issue is researchers not ignoring relevant data. What would you have them do, deliberately ignore that a known vector exists?
Myxobacteria
Yeah, I know. An “extreme example”, right?
They don’t argue against it. The differences are due to the same type of processes taking place within different time and space frames. With this in mind the differences are to be expected.
Both involve an overall expansion of form being held in balance by the forces of growth and decay. The same forces are at work within these different frameworks.
The coordination lies in the balance of nature. For life on earth to have continuously survived requires that the system be in dynamic equilibrium at every stage. We have seen examples of this equilibrium being disrupted when humans introduce foreign species to an ecosystem without understanding the consequences.
Or they are capable of individual physical expression of an overarching dynamic pattern rather than forming through a vast series of accidental changes.
I would say that selection is a force of individuation and drift allows balance to be maintained.
No that’s actually not the default state of bacteria in the wild, but an artifact of how we grow bacteria in lidquid cultures that are constantly shaken and mixed to ensure more effective mixing of nutrients. In their “natural” state bacteria like to stick together in bacterial mats and colonies.
Sorry my mistake, typed million when I meant billion.
You can say whatever you like. But can you actually support any of it? I think not.
Okay, so according to your figures N = “a big number” that you have as the denominator. For the numerator there is either 1 or 8000. And you think that it would make a big difference which one it was. What if N was the number obtained by the amount of combinations in a 63 digit string with 20 choices available in each position? Would it make any significant difference if the numerator was 1 or 8000?
Yes, it would make an 8,000-fold difference.
Whatever the denominator is. This is grade school math.
But if you want to argue that the denominator should be 20^63, you are going to have to demonstrate that we can ignore the effects of selection.
Have at it. Make gpuccio and kairosfocus proud.
I wasn’t chiding you John. I was making a joke. Sorry you didn’t get it. It was never about whether you were right or wrong with your list.
Of course you were. That’s why you waited until just now to tell us.
Isn’t EVERYTHING the magic result of “evolution” (the mystery that no one can see happening)? I hear entropy is not really “disorder”. And how do we get humans and cats when milk and coffee turns invariably light brown with no cats/humans in between?
1. Not about Galton. This nastiness was very strong in the 20th century and is ongoing. Now it’s as simple as IYIs pretending to know what’s “best”. And when the bodies pile up, it’s always someone else’s fault.
2. Coming up. Next OP. Meanwhile, I keep hearing: “this theory might be illogical, but I believe it because you don’t show me an alternative”. Does this claim make sense to you?
3. Semantics? ‘Messy mix’ ≠ ‘Modification’ Clear and simple.
We were talking about “modification”, not “selection”, but that doesn’t work either as shown elsewhere.
4. Soon enough…
Did I not make clear that Swamidass made a stupid claim? Read again. Why don’t you two fight it out. I’ll get the popcorn.