- 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.
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.
It’s unpolite to quote something, and then respond as if you didn’t read what you quoted. I’m not talking just about similar genes Charlie, I’m talking about them plus the surrounding evidence that they come from a different organism, with features that betray their coming from another organism, with features betraying that they jumped along with known, well characterized, mobile elements. That’s elements known to jump from genome to genome across species.
HGT is not an evolutionary pathway, it’s something that happens among life forms. It doesn’t strengthen any belief in how I think evolution happens. It’s but one more thing that happens between life forms, and it happens to provide a different avenue to evolution than what I had understood so far. Nothing about “beliefs” or “desires” on my part. Had you read what I wrote, you’d understand that I wasn’t talking about being convinced “just because” I liked one idea better than another, but because of the evidence, such as particular features of the transferred genes and the sequences surrounding them. If you don’t understand the terminology say so. Then we could clarify meanings, instead of me getting confused as to why, after I explained some pretty evidence, you talk about “jumping” to “HGT” “just because” “it strengthens” some “belief.”
As per your example, transposons are well known jumping sequences. It is well known that they insert themselves across organisms. They’re mobile elements. So I don’t see why you’d assume that the jumping through a vector, such as ticks, is made up to salvage some theory, when scientists have always known that these sequences “specialize” in jumping.
Do you also think that the malaria parasite appears magically in humans, rather than being transmitted by a mosquito from one animal to another? Maybe scientists made up the mosquito vector to salvage some preconceived favourite belief as well there. Right? Evidence? Nah, don’t read about evidence. Hold to your favourite belief, that it’s all made up to salvage evolution, or whatever else that might need saving by making up a mosquito story.
So alluding to some vague “forces of growth and decay” is your idea of going into details?
Or when land bridges between long-separated continents close, or when earth gets completely frozen over during a global glacialiation episode, or when an asteroid smashes into earth killing a decent number of species.
Looks very coordinated. I am sure this had no serious lasting impact and life simply veered back to its original “program” after these minor disruptions.
C’mon Charlie. This is convincing nobody. Contingency is too much of a player to ensure any particular outcome.
Ah, Jeez, this petulant refrain again? No. No, it isn’t.
You hear right. It is a measure of the dissipation of energy. In the case of informational entropy, however, disorder is a closer analogy than it is in thermodynamics (despite the ingrained tendency to treat the latter as such in teaching).
That was probably more clever in your head than it is on the page.
Let’s try an HGT case study. Turn to page 294 in your hymn books (Futuyma, Evolutionary Biology 3rd Ed, Fig 10.24. There’ll be an original paper somewhere, but Futuyma points to a book by Li and Graur as his source). Here we see a case where an anomaly has been ascribed to HGT, in order to ‘save the theory’. A virogene is found in all Old World monkeys, and in some, but not all, cats.
There are several factors to note.
1) This is only an anomaly because it stands out against the rest of the genome, which largely conforms to simple phylogeny – the same phylogeny already broadly established on morphology alone. This is a point repeatedly stated and repeatedly blanked. Even if the virogene moved by ‘magic’, the rest of the genomes in which it sits appear to have been transmitted by vertical descent, because the data forms the hierarchic relations precisely expected from that mode of tranmission.
2) Sequence analysis nests the virogene within the viruses. That is, we know it came from a virus because of the assumption of common descent. See, even anomalies aren’t all that anomalous!
3) Once it transferred, presumably by an ancestor of the small cats catching a bug from a primate, this gene flows into the ‘vertical’ path of descent – it is a heritable change to the genome. And as such, it is a phylogenetic marker for that group. Once again, sequences that are anomalous at one level support common descent at another – because they are just another change, once integrated into the genome.
Of course, I only think all this because of my metaphysical blinders. So, what should I think instead?
Here is an article which argues against the proposal that there are “master regulators” controlling development.
“The uncommon roles of common gene regulatory factors in the genomes of differentiating cells”, by Eric H Davidson:
Gene regulation is achieved by a combination of factors working in a coordinated way.
Davidson made use of data from this article where they comment:…
It has been argued that this amount of TF binding events are due to opportunistic binding, but the article demonstrates that certain genes are specific targets for TF binding.
Genes don’t regulate themselves. The cell regulates its genes in a controlled way.
Is there a pattern of simple vertical descent in prokaryotes?
That guy is making the same semantic mistake that you make. Mistaking the complexity of the machinery for what makes the difference between regulating one thing or another. The concept of a master gene is not that it works all by itself, but that it’s product makes the difference between regulating one thing or another. I do understand that in order for, say, the Bicoid protein to exert its regulatory effects, it combines with a bunch of other proteins (TFs), but it is the presence of Bicoid in the complex that provides the specificity for its binding to start a cascade of regulatory events behind cell differentiation.
There’s no contradiction here. The amount of events can be explained by the presence of opportunistic events, while there must be biologically more meaningful events in the mix as well. That’s what TFs are supposed to be about: specific targets. Otherwise there would be no regulation. What I don’t understand, is what you think this demonstrates. If anything, it makes my point: specific interactions are what I’m talking about, and a lot of the “complexity” we might see otherwise is just noise.
Nothing you cite demonstrates such a thing. How can a cell regulate anything without the tools for such regulation? The tools are proteins, among them TFs. What are these TFs if not the products of genes? What do you think TFs are?
Yes. I would particularly direct your attention to the curious nesting of mitochondria within or near the alpha proteobacteria. Have you encountered this phenomenon … at all … ever … perchance?
Certainly a funny old world when people stop caring about the evolutionary relationships of multicellular eukaryotes, and instead fall back on “But … but … the prokaryotes”!
I think that the interesting issue here is that, suppose that HGT made it pretty much impossible to establish a full, “universal,” vertical history of prokaryotes. Do these guys think that would make evolution false? Do they think all of it hinges on whether or not we can establish a complete history of life by phylogenetic analyses?
I think that’s what’s going on.
However, Charlie seems to mistake problems with establishing a phylogenetic vertical history to whether HGT happens. Since Charlie doesn’t think that HGT happens, then why would he quote from an article that talks about how HGT makes it hard to establish vertical histories for prokaryotes?
Let me return to something that often gets lost in these discussions. Even young earth creationists accept common descent and evolution. So the discussion isn’t really about anyone begin anti-evolution or anti-common descent.
Especially so because prokaryotes are just devolved eukaryotes.
Are you trolling for keiths?
Good to hear.
Really? Do they accept our common ancestry with the rest of the apes, for example?
It doesn’t look that way. Maybe for you it isn’t, but for most creationists it seems, kinda clearly, to be just about that.
So, what is it about for you?
Not according to phylogenetic analysis.
He can do his own trolling, I’m sure …
Entropy has asked whether they accept common descent of humans and apes. They don’t, of course.
We also have had a number of threads here on common descent. The longest one had almost 2,000 comments. The creationists there (or am I supposed to call them “design theorists”?) blatantly refused to accept common descent of, well, anything.
Over at Uncommon Descent there are plenty of people who choose “evolution” as the thing that they are refuting. Cornelius Hunter, for example. There are others who claim to accept “evolution”, though it’s hard to find an example of them accepting common descent of humans and chimps.
Has Mung not noticed any of that? I can come up with lists of UD commenters who reject “evolution” if needed.
You might want to read about microstates and macrostates. Apparently, entropy has nothing to do with disorder.
The question remains: how do you get “humans and cats” from an ever increasing tendency to uniformity?
Did you even read what I wrote? I know. I favour the pedagological approach of Lambert and others.
Because the systems are isolated; there is no general homogenising flow between every organism on earth. Much as there exist lakes at various levels, despite the tendency of water to equilibrate. Or, for that matter, separate cups containing black or milky coffee.
The question to ask would be whether they accept that the various species of apes share a common ancestor, whether they accept that the various species of monkeys share a common ancestor, and whether they accept that the common ancestor of monkeys and the common ancestor of apes share a common ancestor.
Once you find a lineage where they do accept common descent then perhaps ask why they accept shared ancestry in that group. Maybe they accept it for the same reasons you do. And if that ever turns out to be the case, then you could say that you accept the common descent of humans for the exact same reason that they accept common descent of non-humans.
Of course, this requires having an actual conversation and trying to find points of agreement. So the hell with that! 😉
I seem to recall being a part of that thread, and I accept common descent.
I’m sure you can. I see the same thing you do. I think my point is that it is important to try to understand just what it is that they are against. Perhaps by “evolution” they mean universal common descent. Perhaps by “evolution” they mean the ideology.
I doubt that they reject population genetics and changes in gene frequencies. They probably accept at least some speciation (though amazingly many seem not to). And they probably accept at least some common descent. I thik it’s always possible to find that they do in fact accept evolution depending on the questions you ask.
First they’d have to understand a non-strawman version of it, agreed?
It’s quite clear what they think about that. See picture.
Do you see how the lines diverge? That’s common descent.
Yeah but it’s not universal common descent. It is multiple independent descents. Ironically the exact same method they’d use to try to determine which organisms should go together for each of those independent trees, can be applied to all known life as a whole and it’d make perfect sense. There’s zero reason to put their arbitrary lines of separation anywhere.
… and all that divergence has to happen in a few hundred or a few thousand years, if you’re a YEC who is a “baraminologist”. So speciation doesn’t happen before the Creation, but happens at an incredible rate after the Ark lands. And during that period populations change incredibly quickly. They believe in evolution, in fact in hyperevoloution.
I believe that’s Mung’s point. What some creationists call “evolution” and object to is, according to his thesis, universal common descent. Acceptance of limited common descent doesn’t count, to them, as evolution. Of course that’s a nonsensical position, and the devil is in the details of where and how they draw “kind” boundaries. (The answer: between humans and apes, and everything else is up for grabs; the methods are what baraminology is about, and those methods are poorly thought out.)
Haha, the fools! That says ‘Halfric carved these runes’.
So what controls the pattern of Sry expression?
Regulation of male sex determination: genital ridge formation and Sry activation in mice
I don’t think that any bacterium has any idea about anything 🙂
Ah the wisdom of nature! Bacteria, like any wild animal, know instinctively what is appropriate to eat and what they should avoid.
So if it is plausible that the same or similar sequences in distantly related species arrived there due to HGT, does that mean we should believe that all such sequences arrived by the same means? What about the means of echolocation in bats and whales?
There is wisdom inherent in nature.
That’s a nice image of Chondromyces crocatus, heralding the diversification of higher life forms.
It shows the natural tendency of the living world to produce form, a step in the direction of organised multicellularity. The point is not that individual bacteria are diffuse, but that they can survive on their own, independently as viable creatures, something our somatic cells cannot do.
Not extreme, just showing the direction life takes.
Yes but as I said above, they can survive as individuals. And when they form colonies they discharge enzymes and such into the surrounding medium thus acting in a similar fashion to the individual cells in higher organisms.
Selection narrows the range of individual differences within a population to suit the environment. And drift allows for a certain plasticity of the population to cater for fluctuations in the local environment. Giant pandas are endangered because of the effects of selection has restricted their lifestyle and the species lacks plasticity due to their limited numbers.
Whether or not it is present in the genome, of course. Did Professor Google not tell you this?
I don’t recall ever denying that HGT ever happens. What I am saying is that it is provides a convenient explanation. When it is not clear how similar sequences appear in different species then it is easy to assume that it must have happened by HGT. Also any such purported fixation of transferred material is automatically assumed to be accidents of evolution. Organisms tend to be very good at using what is beneficial to them and deiscarding that which is not.
Those that eat the wrong things tend to leave fewer or no descendants. Hey, that sounds like a principle! I wonder if anyone’s thought of it already?
So how come that echolocation’s molecular similarity was not ascribed to HGT?
The difference being that malaria is not inherited as far as I know.
I must say I admire your inventiveness.
But the POINT is that when you claimed that “groups of bacteria at a higher taxonomic level should be treated as equivalent to individual higher animals” you were making a nonsensical proposition.
What unites the cells in an organism is not, as you previously claimed, the potential to exchange genetic material, but a shared genetic interest; they all are closely related and carry (nearly) the same genome. That close genetic relationship is what makes the division of labour profitable in evolutionary terms.
Let me see whether I can follow the part about genetic drift. Genetic drift allows plasticity (by “coping with fluctuations in the local environment”). Pandas are in trouble because they have too little plasticity. That must mean that they have too little genetic drift, which implies that they have too large a population size.
Now actually, pandas have too small a population size, hence by that argument they must have too much genetic drift, and must be too plastic.
I suppose that explains the problems of pandas. One way or the other.
That’s exactly the wrong way around: their limited numbers increases the impact of genetic drift which poses a major concern for conservation, as drift depletes genetic variation and increases the rate of fixation of deleterious mutants.
Noooooooooo, ninja’d again.
Growth and decay are not some vague forces, they are a fundamental feature of life. Binary fission, cell death, apoptosis, photosynthesis, need I go on.
Without growth there would be no life and equally without decay there would be no life. I don’t see what you find vague about that.
I always thought the problems of pandas was their thumb. Times change I guess.
Yeah, I just love the irony of that.
They have a reason Rumraket. You may not like their reason, but they do have one.
Better to try to understand what their reasons are, what your reasons are, and see if any common ground at all can be found, because it not, there are far better ways to spend your time.
Binary fission, cell death, and apoptosis somewhat work as proxies for growth and decay in development (I am giving you a lot of leeway here: apoptosis is programmed, so not really decay). In phylogenesis, not so much, and I am at a loss to name the analogous processes. Spelling those out would help filling in some details.
I certainly don’t know what photosynthesis is doing in your list.
As has been pointed out, drift is greater in small populations than in large ones. And drift also results in less genetic variation, as it ends in fixation. Both drift and selection can result in greater transient variation in the population. Selection of some types — disruptive selection, balancing selection, frequency-dependent selection — can actually result in greater standing variation. So nothing you say is true. And even if it were true it wouldn’t support your original claim. You can pump up your balloon all you like, but it’s still just filled with air.
Photosynthesis is cool. It belongs on any list of cool things.