Signaling Pathways
by BradfordWnt and TGF-β Expression in the Sponge Amphimedon queenslandica and the Origin of Metazoan Embryonic Patterning was published in PLOS One and authored by Maja Adamska, Sandie M. Degnan, Kathryn M. Green, Marcin Adamski, Alina Craigie, Claire Larroux, Bernard M. Degnan.
In tracing an origins trail one finds a pattern emerging and re-emerging. Seeds of functions, fully developed in highly complex eukaryotic organisms, are found conserved in organisms whose genomes have been recently sequenced. The PLOS One paper seeks to trace the origin of developmental signalling systems in sponges through the study of genes that encode Wnt and TGF-β signalling ligands during embryonic development. From the paper:
The origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. While components of many of the major cell signalling pathways have been identified in a range of sponges (phylum Porifera), their roles in development have not been investigated and remain largely unknown. Here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and eumetazoans by studying the expression of genes encoding Wnt and TGF-β signalling ligands during the embryonic development of a sponge.
This next part looks like a primer for front loading innnovations appearing in those early branches of the metazoan tree of life:
The recent sequencing of the genome of the demosponge Amphimedon queenslandica by the Joint Genome Institute greatly facilitates reconstruction of the genetic repertoire that was present in the last common ancestor to all contemporary metazoans and reveals the innovations that lead to evolution of the first branches in the animal tree of life [23]"“[28]. Amongst these innovations must have been a suite of signalling pathways that allow for communication in a range of multicellular contexts, including cell specification and patterning [22]. The highly conserved Wnt and TGF-β signalling pathways are fundamental to a plethora of developmental processes in bilaterian animals. In addition to specification of the first embryonic axes, these pathways interact to specify cells and to pattern tissues in many morphogenetic contexts, ranging from the formation of embryonic organizers [29]"“[32], vertebrate skeleton [33] and the development of limbs in Drosophila and other bilaterians [34]"“[36]. The primacy of Wnt and TGF-β pathways in intercellular communication and cell fate diversification suggests that their evolution may have been concomitant with the origin of multicellularity [22], [37]. Here we address this issue by investigating the expression of Wnt and TGF-β genes during embryonic development in Amphimedon queenslandica. The asymmetrical expression of both genes in Amphimedon embryos indicates that sponges, and hence also the last common ancestor to living metazoans, utilized these two signalling pathways in embryonic patterning.
Signaling genes enabling "communication in a range of multicellular contexts, including cell specification and patterning." Details of front loading continue to unfold.
October 25th, 2007 at 9:31 am
Every seems to be based on a few basic signals as interfaces to a wide variety of functionalities. The same signal (i.e. calcium, phosphorylation etc) can be different depending on the context. Also, the same basic signal (interface) can be refined to include more specific functions.
For instance, the signal/protein/interface that caused polarity in a single cell can give rise to mechanisms that cause polarity in a multicellular organism. The step from a single cell eukaryote to a multicell eukaryote could have been simply made by postponing the telophase: you divide the nucleus but do not complete telophase so the cells stay together. Existing gradient will still stay there and give rise to multicellular polarity.
That would be non-teleological front-loading, no?
Comment by AdR — October 25, 2007 @ 9:31 am
October 25th, 2007 at 11:33 am
Could be. It's a good time to make some points about processes and teleology. I'll do so by way of analogy. We explore the universe we inhabit with the aid of 21st century equipment and rocket propelled vehicles today. There was a time when our universe was limited to the earth itself which needed exploring. Some explorers set out to traverse pathways which yielded notable results. Their explorations were purposeful. They set out with a definite direction in mind and used specific transport mechanisms. They also had a general idea as to what obstacles might be encountered during the journey and brought tools with them to overcome such obstacles.
Despite the teleology obvious in this there were many non-teleological events that influenced the actual specific pathway taken to complete the exploratory journey. The explorers did not anticipate the mountain in their path. Its presence was a non-teleological event that altered the actual pathway taken. So too did rivers and forests. Weather, another series of events, influenced the timing of the exploration.
Biological pathways entail direction. There is a realization of increasingly greater complexity associated with an increase in biological structures and mechanisms found among organisms. There is a directional arrow pointing from biochemicals to unicellular organisms to multi-cellular organisms. Environmental events can alter the pathways a teleological process can take. Properties of cellular biochemicals, can be viewed as non-teleological and influence a teleological process because such processes need not afford purpose and direction to every step and pathway along the route taken. One needs to step back and look at the process as a whole to assess teleology.
Comment by Bradford — October 25, 2007 @ 11:33 am
October 25th, 2007 at 11:45 am
I'm curious about one thing in this discussion: When you talk about an environmental feature (in the example provided, the mountain) being non-teleological, do you mean 'entirely' or just with regards to the process currently in place (the exploration)? I'm tempted to view the environment an organism exists in as potentially being part of a telic process, or at least not utterly distinct from biological development. So I'd imagine the example being those explorers coming across a man-made river they have to cross - they may not have expected the river, and their actions to cross/cope with it may not have been intended originally in their journey, but the river could have been made with the purpose of making any explorers be forced to cross/cope with it. So from one perspective, telic. From another, atelic.
Comment by nullasalus — October 25, 2007 @ 11:45 am
October 25th, 2007 at 12:47 pm
A perfect illustration of one's vantage. People often look at obstacles as something put there to test their faith or fortitude. Yet, the relevant science clearly indicates that mountains arose millions of years ago from natural geological processes without regard to humanity's desires or needs.
There is no scientific evidence that rivers or mountains were formed by telic processes for the moral instruction of the Lewis and Clark expedition. There is no valid empirical prediction that can be formed on the basis of such a claim, just as there is no scientific evidence or empirical prediction that derives from a claim of biological ID.
However, it is natural for people to ascribe meaning to events. There is nothing inherently wrong with finding such meaning in our experiences. Just don't conflate that with science.
Comment by Zachriel — October 25, 2007 @ 12:47 pm
October 25th, 2007 at 1:16 pm
nullasalus:
The mountain was non-teleological with respect to the exploratory pathway as viewed from the perspective of the explorers. The overcoming of the obstacle was telic.
The evidence can lie in the process. There is a continuity to FL that is not present in conventional theories. FL would entail a series of FL markers along life's pathways starting at the outset where the continuity of conventional theories breaks. So serious is the break that we have had to distinguish between evolution and abiogenesis and apply different descriptive terminology to each reflecting the differing mechanisms thought to drive them. In fact it would be overly generous to ascribe a mechanism to abiogenesis.
We can look for and find biological features that were front loaded for a subsequent stage of development. We can also find a basis for a non-arbitrary level of front loading that would have been necessary at the outset. That would be pegged to minimal genomic requirements with respect to functions and specific genes associated with such functions. These are testable concepts.
Comment by Bradford — October 25, 2007 @ 1:16 pm
October 25th, 2007 at 1:26 pm
Actually, the science clearly indicates the process by which mountains formed, and produces no comment - positive or negative - about the purpose of mountains or lack thereof.
Claims that the environment is without purpose is not substantiated by the evidence available. People can discuss meaning as they please, but they shouldn't be allowed to pass scientifically vacuous statements (such as that quoted above) off as science.
Comment by nullasalus — October 25, 2007 @ 1:26 pm
October 25th, 2007 at 1:56 pm
Let me know when you find scientific evidence of those "markers".
Such a purpose would be a random (i.e. orthogonal) variable with regards to mountain formation, hence we are justified in making the scientific statement that they formed "without regard to humanity's desires or needs". While a lottery winner may thank God, we can scientifically demonstrate that there is no correlation between religiosity and winning.
Comment by Zachriel — October 25, 2007 @ 1:56 pm
October 25th, 2007 at 2:14 pm
The purpose or lack of purpose would be equally orthogonal to any consideration in the formation of mountains.
I respect your right to adhere to any religious belief you choose, but it does not justify your misleading statements on what has been scientifically demonstrated - and talk of being able to test for design in the formation of mountains is scientifically vacuous.
Comment by nullasalus — October 25, 2007 @ 2:14 pm
October 25th, 2007 at 2:19 pm
The evolutionary markers would be those discussed by Mike et. al. in numerous posts. Those relevant to the initial front load would be found through studies of minimal genomes.
Comment by Bradford — October 25, 2007 @ 2:19 pm
October 25th, 2007 at 3:16 pm
I just thought this bears repeating:
However, it is natural for people to ascribe meaning to events. There is nothing inherently wrong with finding such meaning in our experiences. Just don't conflate that with science.
Comment by Zachriel "” October 25, 2007 @ 12:47 pm
Our experiences are meaningless wrt science?!
(Dagon, protect me!)
Comment by Rock — October 25, 2007 @ 3:16 pm
October 25th, 2007 at 3:18 pm
Yes, of course. There is no correlation and ample non-telic explanations.
Maybe Vulcan really does cause mountains to rise up when he is angry. But there is no scientific evidence to support such a view. He is an extraneous entity. From a scientific vantage, mountains form "without regard to Vulcan's desires or needs".
Comment by Zachriel — October 25, 2007 @ 3:18 pm
October 25th, 2007 at 3:26 pm
Nothing I've seen. MikeGene has stated that the evidence "spawns a genuine suspicion."
Comment by Zachriel — October 25, 2007 @ 3:26 pm
October 25th, 2007 at 3:28 pm
The process of determining what evidence is scientific and/or relevant to the hypothesis one is hoping to support……. is that a logical/objective process?
Comment by Doug — October 25, 2007 @ 3:28 pm
October 25th, 2007 at 3:34 pm
Rock:
One can utilize teleology with respect to biology without proceeding to metaphysical speculations. The following has been widely quoted:
Purpose generally can be substituted for the term function without affecting the concept discussed.
Comment by Bradford — October 25, 2007 @ 3:34 pm
October 25th, 2007 at 3:49 pm
According to your religious belief, yes. I'm glad you agree with me.
And the idea that environments and reality as a whole unfolds without intelligent causation behind them is scientifically vacuous - there is no way to test for it, no falsifiability, and the postulation is an anchor to scientific inquiry.
You've come a long way, Zachriel. I'm proud of you.
Comment by nullasalus — October 25, 2007 @ 3:49 pm
October 25th, 2007 at 4:09 pm
Just make specific and distinguishing empirical predictions that are entailed in the hypothesis. We call it "data".
What are my religious beliefs? And why would they be relevant to a scientific discussion?
Vulcan has no scientific merit as an explanation of geological phenomena.
My views have not changed during the course of this thread.
Comment by Zachriel — October 25, 2007 @ 4:09 pm
October 25th, 2007 at 4:25 pm
They aren't relevant to a scientific discussion. In fact, they offer nothing to such a discussion. We've been over this:
You did agree with me, after all.
Denial of any intelligence(s) behind geological phenomena get us nowhere. Alluding to their lack is scientifically vacuous, and not necessary to explain the data.
Then you've been in agreement with me all this time? Interesting miscommunication, but it does happen. Telic forces can be misunderstood after all.
Comment by nullasalus — October 25, 2007 @ 4:25 pm
October 25th, 2007 at 5:03 pm
If someone proposes a hypothesis, such as intelligent causation, then we use the hypothesis to form empirical predictions (assuming the claim of intelligent causation can be formed in such a way as to entail empirical predictions). We test these predictions to determine the validity of the original claim.
We're not actually that far apart. We can't falsify some nebulous claim of intelligent causation, only sufficiently well-defined claims.
Comment by Zachriel — October 25, 2007 @ 5:03 pm
October 25th, 2007 at 5:24 pm
How does a hypothesis entail a specific and distinguished empirical prediction? Data can be conformed to any various competing hypotheses. The subjective, human decision has to be made regarding which hypothesis fits better with the data. People (scientists) ascribe meaning to these results (or events) - but I hope this doesn't get conflated with science. Wait a minute…..
Zach, it appears your reasoning runs into a snare.
When is it appropriate to ascribe meaning to events/results in order for those ascriptions to be considered scientific?
Comment by Doug — October 25, 2007 @ 5:24 pm
October 25th, 2007 at 6:50 pm
A scientific hypothesis is a tentative assumption made in order to draw out and test its empirical consequences. Most hypotheses derive from well-established theories.
For example, let's hypothesize that the Earth is rotating. If the Earth is rotating, it should bulge at the equator. If it bulges at the equator, then pendulums should swing slower there (Newton). In order to test this prediction, we simply take measurements at different latitudes (Halley). As a bonus, if confirmed, this would give us an approximate measure of the bulge (Newton).
A good scientific hypothesis is capable of making specific and distinguishing predictions of empirical phenomena. The more specific the predictions, the more varied the predictions, the stronger our confidence is in our conclusions. Then as we build our confidence, we develop new hypotheses to extend our knowledge.
The Scientific Method
Comment by Zachriel — October 25, 2007 @ 6:50 pm
October 26th, 2007 at 9:50 am
A hypothesis does none of this - predictions/explanations/accuring supporting data is performed by the human. You're trying to remove the human role from the scientific method and you're going to fail. Data underdetermines any hypothesis. There is no logical link that exists between a set of data and a particular hypothesis, nor between a static hypothesis and a prediction of a future outcome.
Comment by Doug — October 26, 2007 @ 9:50 am
October 26th, 2007 at 9:54 am
A scientific hypothesis is a tentative assumption made in order to draw out and test its empirical consequences. That's the definition. Most hypotheses derive from well-established theories. If the tentative assumption does not entail empirical consequences, then it is not a valid scientific hypothesis.
Data may underdetermine a *theory*. A scientific hypothesis is a specific assertion that has empirical consequences.
Of course there is. I even provided an example derived from theory. Every scientific paper of note begins with a hypothesis followed by an observational attempt to verify or contradict the prediction.
Comment by Zachriel — October 26, 2007 @ 9:54 am
October 26th, 2007 at 2:49 pm
Zach, are you saying this to a logical link existing between data and a particular hypothesis?
Comment by Doug — October 26, 2007 @ 2:49 pm
October 26th, 2007 at 2:51 pm
I want this question separate from the one above. That's why I created two consecutive posts.
Do those predictions/consequences prove the hypothesis to be correct?
Comment by Doug — October 26, 2007 @ 2:51 pm
October 26th, 2007 at 8:51 pm
The Scientific Method
Yes, there is a deductive link. If
HypothesisthenPrediction. That's why the scientific method is often called hypothetico-deductive. Try looking at the example again.No. Science does not deal in proof, but in evidence. However, if Newton can predict the retardation of a pendulum thousands of miles away, then we gain a measure of confidence in Newton's Theory. From Halley's measurements, Newton calculated the Earth's equatorial bulge. Then others measured that bulge with other methodologies to verify and refine that initial calculation. We gain confidence with each verified prediction, especially when from varied methods and areas of study. So we have detailed calculations of planetary orbits, detailed studies of mechanics on Earth, the retardation of the pendulum, and careful surveying techniques to verify the equatorial bulge. At some point, to deny the Earth's rotation would be without scientific merit.
Comment by Zachriel — October 26, 2007 @ 8:51 pm