Quote (Soapy Sam @ Oct. 18 2013,13:04)WJM: Quote Atheistic materialism is a rebellion against the obvious. Only a fool can look at the nanotechnological marvels in a single cell and say “There is no design necessary here.”
That's that settled then <dusts hands>. Science can go home; it's obvious.
That evolutionary limits appear throughout the cell--more evidence of design.
After all, humans sometimes make things look accidental. Well, sorta, a little. You can almost always tell. But see, this is a super-designer--not necessarily God, but certainly within that sort of capability--so you can't discern the difference between evolution and design.
That's how designed it is. God/not-God is whimsical--as are his followers, like happy-go-lucky William--and thought, screw it, I'll make everything look evolved, since it's the only non-design process that could make complex organisms. If that doesn't bespeak my power and ability, what the fuck could?
And you all thought there would be nothing to teach in an ID course.
People who think sharks are "primitive" fish may be commended as being reasonably up-to-date with the evolutionary literature, but they need to take note of a new fossil fish that has thrown all the ideas into the melting-pot. Only a year ago, as an apparently coherent story was beginning to emerge, a specialist in vertebrate biology explained that the common ancestor of all jawed vertebrates on Earth resembled a shark.
"The common ancestors of all jawed vertebrates today organized their heads in a way that resembled sharks. Given what we now know about the interrelatedness of early fishes, these results tell us that while sharks retained these features, bony fishes moved away from such conditions." (Source here)
Fossil plus restoration of Entelognathus (source here)
There are four groups of early fish: the extinct Acanthodians and Placoderms, and the extant Chondrichthyes (sharks, rays and ratfish) and Osteichthyes (bony fish). It is the interrelationships of these groups that is much discussed by evolutionary scientists, and work in recent years has tended to see the Acanthodians as either a very early relative of sharks, or close to the common ancestry of all modern jawed vertebrates (for more on this, go here). The placoderm fishes had bony skulls and simple beak-like jaws built out of bone plates. This seemed to position them some way from the other groups, and it was widely thought that placoderm features bore little or no relation to the Osteichthyes.
"[Palaeontologists] thought that the last common ancestor of living jawed vertebrates had no distinct jawbones - that it was similar to a shark, with a skeleton made mostly of cartilage and at most a covering of little bony plates. The theory went that the bony fishes evolved later, independently developing large facial bones and inventing the 'modern' jaw. Such fishes went on to dominate the seas and ultimately gave rise to land vertebrates."
However, a major placoderm find from the Upper Silurian in China has stimulated a remarkably different interpretation. The fish, which has been given the name Entelognathus, appears initially to be a typical placoderm. The surprise comes when looking closely at the jawbones.
"When examined from the side, however, Entelognathus reveals itself as anything but expected. Absent are gnathal plates - simple jawbones characteristic of placoderms. Instead, the mouth is rimmed with bones that integrate with the cheek plates, the lower jaw is composed of an elongated 'box' of bony plates and cartilage, and the throat and gills are clad in a series of articulating plates. Both in the overall pattern and the specific detail of these plates, the fossil showcases traits that were once considered diagnostic of bony fishes, and entirely unknown in placoderms. Entelognathus, it seems, is a placoderm with a bony-fish-like grin." (Source here)
The jawbones are of great importance because they are much more complex than the single bone found in other placoderms. It is a case of abrupt appearance of complexity. Furthermore, this complexity is found in the Osteichthyes, but not in the Acanthodians or Chondrichthyes. There are two alternative evolutionary explanations: the first is that Entelognathus is ancestral only to Osteichthyes, and the second is convergence. It is the remarkable (jaw dropping) nature of the similarity of structure that has convinced most specialists that this find requires a re-writing of the evolutionary tree. This is how John Long puts it in a blog post, which headlines the thought that this new fossil is a missing link:
"But its lower jaw is composed of a complex set of bones, unlike other placoderms whose jaw was made of a single bone. This pattern of bones in Entelognathus precisely matches those in the lower jaw of early fossil bony fish (osteichthyans). Entelognathus also possessed special bones underneath its lower jaws called gulars, which are today only found in bony fishes. This fish shows the first appearance of the dentary bone which is found in all bony fishes, amphibians, reptiles and mammals. It is the very same bone in our lower jaw. The new discovery from China gives us powerful new insights about the building of the human body plan, which began seriously with these ancient fossil fishes." (Source here)
Whether there is a line of descent from placoderms to osteichthyans, or whether the jaw structures originated independently, there are important implications for phylogenies. Instead of sharks being "primitive", they should be regarded as "derived". The implication is that a classic scenario in vertebrate evolution is inverted. Friedman and Brazeau write in their commentary:
"[T]wo things are clear from the various possibilities proposed in their evolutionary tree. First, Entelognathus always branches outside the radiation of living jawed vertebrates, meaning that key components of the osteichthyan face are no longer unique innovations of that group. Second, acanthodians - that pivotal assortment of extinct shark-like fishes - are shifted, en masse, to the branch containing the cartilaginous fishes. This triggers a cascade of implications. If all acanthodians are early cartilaginous fishes, then their shark-like features are not generalities of jawed vertebrates, but specializations of the cartilaginous-fish branch. The most recent common ancestor of jawed vertebrates was thus probably clad in bony armour of the sort common to both placoderms and bony fishes."
A particularly interesting aspect of this "piscine mash-up" are comments on "how did we get it so wrong?" The indications are that cultural factors have been very prominent. The culture is that of progressivist thinking linked to the "Great Chain of Being" approach to looking at the world. A previous blog has explored this theme and can be consulted here. This new fossil is not just raising immensely important issues for cladistic analysis, but also is providing a case study of the human face of science - we find the continuing influence of Aristotelianism and other cultural agendas, despite assurances of science being objective and evidence-based. Friedman and Brazeau again:
"The status of sharks as surrogate ancestors seems well established, but this is an illusion of dogmatic repetition combined with spurious portrayals of present-day cartilaginous fishes as unchanged "living fossils". The popular model of a shark-like ancestor is, in the end, more a hangover of the "great chain of being" of ancient philosophy and pre-Darwinian archetypes than a product of modern comparative biology and phylogenetic "tree thinking". Added to this conceptual inertia is a historically compartmentalized approach to studying early vertebrate groups that made it too easy to dismiss shared similarities - the head and shoulder exoskeleton of placoderms and bony fishes, for example - as independent innovations without adequate evidence."
What we are seeing in the Palaeozoic fish fossils is a mosaic of character traits that are proving very difficult to portray in an evolutionary phylogeny. This is a good reason for at least considering the value of design-thinking and the potential for understanding some of this variability using the concept of phenotypic plasticity.
A Silurian placoderm with osteichthyan-like marginal jaw bones
Min Zhu, Xiaobo Yu, Per Erik Ahlberg, Brian Choo, Jing Lu, Tuo Qiao, Qingming Qu, Wenjin Zhao, Liantao Jia, Henning Blom & You'an Zhu
Nature, 502, 188-193 (10 October 2013) | doi:10.1038/nature12617
The gnathostome (jawed vertebrate) crown group comprises two extant clades with contrasting character complements. Notably, Chondrichthyes (cartilaginous fish) lack the large dermal bones that characterize Osteichthyes (bony fish and tetrapods). The polarities of these differences, and the morphology of the last common ancestor of crown gnathostomes, are the subject of continuing debate. Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes. A phylogenetic analysis places the new form near the top of the gnathostome stem group but does not fully resolve its relationships to other placoderms. The analysis also assigns all acanthodians to the chondrichthyan stem group. These results suggest that the last common ancestor of Chondrichthyes and Osteichthyes had a macromeric dermal skeleton, and provide a new framework for studying crown gnathostome divergence.
A jaw-dropping fossil fish
Matt Friedman & Martin D. Brazeau
Nature, 502, 175-177 (10 October 2013) | doi:10.1038/nature12690
The ancestors of modern jawed vertebrates are commonly portrayed as fishes with a shark-like appearance. But a stunning fossil discovery from China puts a new face on the original jawed vertebrate.
Quote (GaryGaulin @ Oct. 18 2013,13:09) Quote (Jim_Wynne @ Oct. 18 2013,12:55)I asked if your program creates intelligence or simulates it...
In your words: What's the difference?
That's your problem!
Quote (Quack @ Oct. 18 2013,02:02)I only wonder how Gary explains artficial breeding, i.e. human breeding and animal husbandry. Plants and animals have undergone significant changes during the past 10 - 20 thousand years.
Is that caused by intelligent cells and molecules, or are humans the operating agent, as a stand-in for natural selection?
To me, it looks like evolution has very little with intelligence to do and lots with genetics, environment and natural selection to do.
A much more current and precise explanation is contained in information on page 8, in the "Features of the Universe and of Living Things" section:
Quote Also from space, giant beaver dams are visible. These dams provide still deep water to protect against predators and to float food and building material. Beavers build their homes (also called lodges) in the resulting pond. Lodges have underwater entrances to prevent entry by any other animal but have been filmed living with smaller muskrats who have similar lodge building habits (See: David Attenborough: Beaver Lodge Construction Squad - BBC Earth) sharing the inside of the lodge with the beavers who made them.
To impress a mate, the male bowerbird constructs a large (for their size) colorfully adorned (aesthetic) bower to impress a companion (See: David Attenborough - Animal behaviour of the Australian bowerbird - BBC wildlife). Without knowledge of the male bowerbird’s skills a paleoanthropologist can easily assume that their aesthetically optimized shelter is a human shrine to a deity who lives in an adorned little hut. Or conclude that there were once such tiny humans. The construction would be too complicated for a child to build but where thought to be a doll-house built by an early human craftsman might be scaled up by scientists to show what an early human dwelling looked like.
Intelligent behavior of living things determines where they live, what they partner with, feed on, or hide from. And teamwork of living things has led to complex social populations who together are very successful at controlling their environments. Others around them can quickly be forced to find a new strategy, in response to theirs.
At all levels of complexity living things profoundly change each other and environment in response to each other’s behavior in ways that make it impossible to explain the origin of one without including all other living things around them. As in Social Learning Theory, there is reciprocal causation where the person (or living thing), the behavior, and the environment can have an influence on each other (A influences B and B influences A).
What grazes in an intelligence produced pasture depends on what kind of living thing the intelligent farmers are. We at the multicellular intelligence level have our farm plants and animals such as cows and chickens, along with animals physically able to help with farm chores. For single celled social amoebas (slime mold) the livestock it raises is a special kind of bacteria. When unfavorable conditions produce famine instead of eating them all they save some to store as seed (spores) inside a protective capsule they construct so at least some in the colony survive to reestablish itself again later. Environments where bacteria are raised includes inside of sea creatures, where an impressive self-lighting system is made by coordinated group actions of cultivated bacteria.
At our level, we have our farm plants and animals such as cows and chickens. And there are many animals physically able to help with farm chores including catching of rats (ratters) but if they do not want to live among humans then they will stay away. A dog (possibly wolf) with controlling (of other animals) behavior might enjoy protecting and herding the animals for a human farmer. One of any size or breed with a behavior to be a good ratter will prefer being on guard near the food supply all the rats are after. Where it is unhappy with living conditions the dog may run off to another human settlement where conditions are better, then another human group benefits from the dog’s presence.
What could outrun a human might not outrun their dog. Here there is a partnership not even of the same species but since both are highly social animals each still sees each other as “part of the family” or as the dog would see it “part of the (wolf) pack”. Sneaking up on them while sleeping is virtually impossible where one barks at even the mice and the others have hunting weaponry of one form or another to take care of the larger intruders. Early pioneers of the US and before knew it was a good idea to make one a priority to have with the family when out in the wilderness. So our arms and hands may not be good for running but the dog that is would just as well the human build the warm dwelling for them, because they sure don’t know how to with their paws.
Dogs that have through time done very well in a farming community do not always work well as a house pet. For example one that is born to be an excellent ratter can easily rip a house to shreds trying to dig for them in anything that smells ratty, even the furniture. Dogs that need to run do not like to be in a small space, and ones that are very controlling will only have the human family to dominate which often becomes a fight to the finish that one way or another ends at the veterinarian’s office. Taking away the ability for a living thing to find a stable environment where they belong is harmful to it personally and over time to its entire breed/species.
At the molecular and cellular scale intelligence inherently optimizes what it can control therefore convergence on a near optimal biological design for conditions is expected, predicted. Each design is suited for the environment it's for. The cephalopod (octopus, squid, cuttlefish) eye is well designed for a cephalopod. Our eye is well designed for us.
The extinction of the long enduring dinosaurs may have mostly been caused by design limitations that made it impossible for them to forever keep up with optimization of insects and pathogens. Asteroids falling or not, given their possible vulnerabilities to pathogens the extinction of dinosaurs might be predictable, as well as the emergence of better adapted to pathogens biological designs such as ourselves to in time becoming a significant feature of a planet such as this. Where repeated on another planet with these conditions, there could be similar plants and animals that would tend to go extinct all at once when environmental change they in the past easily endured stresses them into extinction.
Living things change each other in response to each other’s behavior in ways that make it hard to explain the origin of features of one without including features of all living intelligent things around them, all the way to the molecular level to the viruses. Without this life-giving interconnected intelligent causation from nonrandom behavior of matter the planet would likely be just another lifeless carbon dioxide world, so profoundly different that not even the weather could ever be the same anymore.
 Slime moulds bet the farm on survival - life - 19 January 2011 - New Scientist, “Primitive agriculture in a social amoeba”, Debra A. Brock, Tracy E. Douglas, David C. Queller & Joan E. Strassmann
Nature, Volume: 469, Pages: 393–396, 20 January 2011, doi:10.1038/nature09668
 Bonnie Bassler on how bacteria talk, TED Video:
Quote (GaryGaulin @ Oct. 18 2013,13:09) Quote (Jim_Wynne @ Oct. 18 2013,12:55)I asked if your program creates intelligence or simulates it...
In your words: What's the difference?
If you don't see this as a significant question, or worse, if you can't answer it, you're further gone than I thought.
"Materials submitted to the Texas Education Agency and examined by the Texas Freedom Network and university scientists show that publishers are resisting pressure to undermine instruction on evolution in their proposed new high school biology textbooks for public schools," according to a press release issued by the Texas Freedom Network on October 16, 2013.
The Next Generation Science Standards avoided a potential obstacle in Kentucky when the Interim Joint Committee on Education decided not to address the issue of their adoption, according to WFPL radio in Louisville, Kentucky (October 15, 2013).
"Why can't science teachers simply teach science?" was the reaction of a columnist for the Charleston, South Carolina, Post and Courier (October 13, 2013), in the wake of the state board of education's discussion of the revised state science standards at its October 9, 2013, meeting.
"The state Board of Education gave initial approval to a new set of science standards Wednesday, although some board members tried to overturn the vote out of concern over whether the new guidelines leave room for students' religious beliefs on the origin of life," reported the Greenville News (October 9, 2013).