Interesting proteins: DNA-binding proteins SATB1 and SATB2

_{Giuseppe Puccio

July 14, 2017

Intelligent Design}

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With this OP, I am starting a series (I hope) of articles whose purpose is to present interesting proteins which can be of specific relevance to ID theory, for their functional context and evolutionary history.

DNA-binding protein SATB1

SATB1 (accession number Q01826) is a very intriguing molecule. Let’s start with some information we can find at Uniprot, a fundamental protein database, about what is known of its function (in the human form):

Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma

And:

Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes

IOWs, it is an important regulatory protein involved in many different, and not necessarily well understood, processes, which binds to DNA and in involved in chromatin remodeling.

It is also involved in hematopoiesis (especially in T cell development), and has important roles in the biology of some tumors:

Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis.

Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis.

Keywords for molecular function: Chromatin regulator, DNA-binding, Repressor

Now, some information about the protein itself. I will relate, again, to the human form of the protein:

Length: 763 AAs. It’s a rather big protein, like many important regulatory molecules.

Its subcellular location is in the nucleus.

It is a multi-domain protein, with at least 5 detectable domains and many DNA binding sites.

Evolutionary history of SATB1

Now, let’s see some features of the evolutionary history of this protein in the course of metazoa evolution.

I will use here the same tools that I have developed and presented in my previous OP:

The amazing level of engineering in the transition to the vertebrate proteome: a global analysis

So, I invite all those who are interested in the technical details to refer to that OP.

Here is a graph of the levels of homology to the human protein detectable in other metazoan groups, expressed as mean bitscore per aminoacid site:

Fig. 1: Evolutionary history of SATB1 by human-conserved functional information

The green line represents the evolutionary history of our protein, while the red dotted line is the reference mean line for the groups considered, as already presented in my previous post quoted above (Fig. 2).

As everyone can see, this specific protein has a very sudden gain in human-conserved information with the transition from pre-vertebrates to vertebrates. So, it represents a very good example of the information jump that I have tried to quantify globally in my previous post.

Here, the jump is of almost 1.5 bits per aminoacid site. What does that mean?

Let’s remember that the protein is 763 AA long. Therefore, an increase of information of 1.5 bits per aminoacid corresponds to more than 1000 bits of information. To be precise, the jump from the best pre-vertebrate hit to the best hit in cartilaginous fish is:

1049 bits

But let’s see more in detail how the jump happens.

I will show here in detail some results of protein blasts. All of them have been obtained using the Blastp software at the NCBI site:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

with default settings.

Here is the result of blasting the human protein against all known protein sequences except for vertebrate sequences:

Fig. 2: Results of blasting human SATB1 against all non vertebrate protein sequences

As can be seen, we find only low homologies in non vertebrates, and they are essentially restricted to a small part of the molecule, that correspond to the first two domains in the protein, or just to the first domain. The image shows clearly that all the rest of the sequence has no detectable significant homologies in non vertebrates (except for a couple of very low homologies for the third domain).

The best hit in non vertebrates is 154 bits with Parasteatoda tepidariorum, a spider. Here it is:

Fig. 3: The best hit in non vertebrates (with a spider)

The upper line (Query) is the human sequence. The bottom line (Sbjct) is the aligned sequence of the spider. In the middle line, letters are identities, “+” characters are similarities (substitutions which are frequently observed in proteins, and are probably quasi-neutral), and empty spaces are less frequent substitutions, those that are more likely to affect protein structure and function if they happen at a functionally important aminoacid site.

The alignment here is absolutely restricted to AAs 71 – 245 (the first two domains), and involves only 177 AAs. Of these, only 78 (44%) are identities and 111 (62%) are positives (identities + similarities). So, in the whole protein we have only 78 identities out of 763 (10.2%).

The spider protein is labeled as “uncharacterized protein”, and that is the case in most of the other non vertebrate hits.

All the other non vertebrate hits, with a couple of exceptions, are well below 100 bits, most of them between 70 and 86 bits.

IOWs, the protein as we know it in vertebrates essentially does not exist in non vertebrates.

Even non vertebrate deuterostomia, which should be the nearest precursors of the first vertebrates, have extremely low homology bitscores with the human protein:

Saccoglossus kowalevskii (hemichordates): 87 bits

Branchiostoma floridae (cephalochordate): 67 bits

The information jump in vertebrates

Now, what happens with the first vertebrates?

The oldest split in vertebrates is the one between cartilaginous fish and bony fish (from which the human lineage derives). Therefore, homologies that are conserved between cartilaginous fish and humans had reasonably to be already present in the Last Common Ancestor of Vertebrates, before the split between cartilaginous fish and bony fish, and have been conserved for about 420 million years.

So, let’s see the best hit between the human protein and cartilaginous fish. It is with Rhincodon typus (whale shark). Here it is:

Fig. 4: The best hit of human SATB1 in cartilaginous fish (with the whale shark)

Here, the alignment involves practically the whole molecule (756 AAs), and we have 1203 bits of homology, 603 identities (79%), 659 positives (86%).

IOWs, the two molecules are almost identical. And the homology is extremely high not only in the domain parts, but also in the rest of the protein sequence.

Now, the evolutionary time between pre-vertebrates and the first split in vertebrates is certainly rather small, a few million years, or at most 20 – 30 million years. Not a big chronological window at all, in evolutionary terms.

However, in that window, this protein appears almost complete. 603 aminoacids are already those that will remain up to the human form of the protein, and only 78 of them were detectable in the best hit before vertebrate appearance.

1049 bits of new, original functional information. In such a short evolutionary window.

Functionality

Why functional? Because those 603 aminoacid have remained the same thorugh more than 400 million years of evolution. They have evaded neutral or quasi neutral variation, that would have certainly completely transformed the sequence in such a big evolutionary time, if those aminoacid sites were not under extreme functional constraint and purifying (negative) selection.

Now, I say that this fact cannot in any way be explained by any neo-darwinian model. Absolutely not.

Moreover, there is absolutely no evidence in the available proteome of any intermediate form, of any gradual development of the functional sequence that will be conserved up to humans (except, of course, for the 50 – 78 AAs which are already detectable in the first two domains in many pre -vertebrates).

By the way, Callorhincus milii, the Elephant shark, has almost identical values of homology:

1184 bits, 599 identities, 654 positives

But, how important is this protein?

In the ExAC database, a database of variations in the human genome, missense mutations are 110 out of 260.3 expected, with a z score of 4.56, an extremely high measure of functional constraint.

The recent medical literature has a lot of articles about the important role of SATB1 at least in two big fields:

T cell development
Tumor development (many different kinds of tumors)

If we want to sum up in a few words what is known, we could say that SATB1 is considered a master regulator, essentially a complex transcription repressor, involved mainly (but not only) in the development of the immune system, in particular T cells. A disregulation of this protein is linked to many aspects of tumor invasivity (especially metastases). The protein seems to act, among other possibilities, as a global organizer of chromatin states.

Here is a very brief recent bibliography:

Essential Roles of SATB1 in Specifying T Lymphocyte Subsets

SATB1 overexpression correlates with gastrointestinal neoplasms invasion and metastasis: a meta-analysis for Chinese population

SATB1-mediated Functional Packaging of Chromatin into Loops

DNA-binding protein SATB2

But there is more. There is another protein which is very similar to SATB1. It is called DNA-binding protein SATB2 (accession number Q9UPW6).

Its length is very similar to SATB1: 733 AAs.

Uniprot describes its function as follows:

Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes

Which is very similar to SATB1. But now come the differences. While SATB1 is implied prevalently in T cell development and tumor development, SATB2 is:

Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation

So, similar proteins with rather different specificities. While SATB1 is mainly connexted to adaptive immunity (T cell development), SATB2 seems to be more linked to neuronal development. Like SATB1, it is involved in cancer development, although usually in different types of cancer.

Here is a brief recent bibliography about SATB2:

Mutual regulation between Satb2 and Fezf2 promotes subcerebral projection neuron identity in the developing cerebral cortex

SATB1 and SATB2 play opposing roles in c-Myc expression and progression of colorectal cancer

However, how similar is SATB2 to SATB1 in terms of sequence homology?

Here is a direct blast of the two human molecules:

Fig. 5: Blast of human SATB1 vs human SATB2:

OK, they are very similar, but… only 460 identities, 550 positives, 854 bits. IOWs, these two human proteins are similar, but not so similar as the two sequences of SATB1 in the shark and in humans.

Now, here is the evolutionary history of SATB2:

Fig. 6: Evolutionary history of SATB2 by human-conserved functional information

As everyone can see, it is almost identical to the evolutionary history of SATB1. To see it even better, Fig. 7 shows the two evolutionary histories together (the green line is SATB1, the brown line is SATB2):

Fig. 7: Evolutionary history of SATB1 and SATB2 by human-conserved functional information

In particular, pre-vertebrate history and the jump in cartilaginous fish are practically identical. And yet these are two different molecules, as we have seen, with different specificities and about one third of difference in sequence.

Now, let’s blast human SATB2 against cartilaginous fish. Again the best hit is with the whale shark:

Fig. 8: The best hit of human SATB2 in cartilaginous fish (with the whale shark)

And the numbers are very similar, incredibly similar I would say, to those we found for SATB1:

1197 bits, 592 identities, 662 positives.

But what if we blast SATB1 of the whale shark against SATB2 of the whale shark?

Here are the results:

Fig. 9: Blast of whale shark SATB1 vs whale shark SATB2:

Now, please, compare the numbers we got here with those from the similar blast between the two proteins in humans:

SATB1 human vs SATB2 human: 460 identities, 550 positives, 854 bits

SATB1 shark vs SATB2 shark: 468 identities, 556 positives, 856 bits

Almost exactly the same numbers! Wow!

What does that mean?

It means that this system of two similar proteins with different function arises in vertebrates as a whole system, already complete, with the two components already differentiated, and is conserved almost identical up to humans. Indeed, SATB1 and SATB2 have the same degree of homology both in sharks and in humans, and the two SATB1 proteins in shark and humans, as well as the two SATB2 proteins in shark and humans, have greater similarity, after more than 400 million years of divergence, than SATB1 and SATB2 show when compared, both in sharks and in humans.

Would you describe that as sudden appearance of huge amounts of functional information, followed by an extremely long stasis? I certainly would!

The following table sums up these results:

Sequence 1	Sequence 2	Bitscore
SATB1 Human	SATB2 Human	854
SATB1 Shark	SATB2 Shark	856
SATB1 Human	SATB1 Shark	1203
SATB2 Human	SATB2 Shark	1197

IOWs, the whole system appeared practically as it is today, before the split of cartilaginous fish and bony fish, and has retained its essential form up to now.

So, the total amount of new functional information implied by the whole system of these two proteins is about 1545 bits (considering 855 bits of common information, and 345 bits x 2 of specific information in each molecule).

An amazing amount, for a system of just two molecules, considering that 500 bits is Dembski’s Universal Probability Bound!

Let’s remember that in my previous post, quoted above, I showed that the informational jump from pre-vertebrates to vertebrates is more than 1.7 million bits. That’s a very big number, but big numbers sometimes are not easily digested. So, I believe that seeing that just two important molecules can contribute for almost 1500 bits can help us understand what we are really seeing here.

Moreover, it’s certainly not a case that those two molecules seem to be fundamental in two very particular fields:

a) The adaptive immune system

b) The nervous system

if we consider that those are exactly the two most relevant developments in vertebrates.

And, as a final note, please consider that these are very complex master regulators, which interact with tens of other complex proteins to effect their functions. The whole system is certainly much more irreducibly complex than we can imagine.

But still, just the analysis of these two sister proteins is more than enough to demonstrate that the neo Darwinian paradigm is completely inappropriate to explain what we can see in the proteome and in its natural history. And this is only one example among thousands.

So, I want to conclude repeating again this strong and very convinced statement:

The observed facts described here cannot in any way be explained by any neo-darwinian model. Absolutely not. They are extremely strong evidence for a design inference.

Comments

Insightful quote: "Categorization is the grouping of different things according to some common trait. But we must remember that they are different things."Dionisio_{July 15, 2017
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Mung: No, I don't believe it, as you probably know... :) Domains are an important concept, and an useful way to classify functional units according to sequence similarity, structure similarity and function similarity. But we must look at them for what they are: a gross categorization. If we think of them as fixed, rigid modules, we miss the point: it's just oversimplification. Categorization is the grouping of different things according to some common trait. But we must remember that they are different things. Our understanding of protein structure is gross at best. We analyze proteins as a medical examiner analyzes a corpse. We know little of how proteins really work. Domain homology has been vastly used by darwinists to trace connection throughout evolutionary history. That's fine. But connections are not explanations. Sequences change and sequences are conserved. both in domains and outside of them. Some changes are functional, others certainly are not. But it is difficult to discriminate. I have always tried to emphasize that differences often tell more than homologies. It's the sum total of differences and homologies that can reveal the general plan, provided that we don't look at it through the eyes of ideology. Darwinists love to oversimplify things, because their theory hates too much complexity. But really, do you think that LEGO could be satisfactorily explained by a darwinist context? :)gpuccio_{July 15, 2017
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So, gpuccio, you don't believe that evolution works by mixing and matching protein domains in order to see what new and useful arrangements might arise? Sort of like a 6 year old with a nice assortment of LEGO parts.Mung_{July 15, 2017
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john_a_designer: Thank you for your comments. I agree. The problem is that darwinists have become so accustomed to "explain" things by just building a narrative compatible with their theory, that they really believe, after decades of absolute power in the academy, that building a narrative is an explanation. They are not bothered by the complete absence of empirical support to their narratives. They are not bothered by the mathematical and probabilistic impossibilities implicit in the theory itself. A narrative is an explanation, provided that it is their won narrative, and that it supports their own theory. But an explanation is all another thing. An explanation must contribute to our understanding, must be formally appropriate, must correspond to what facts are saying. Let's compare these two statements: a) These two proteins are complex master regulators. They share a lot of functional specificity, including the ability to bind DNA at some specific region, and they share a great part of their sequence, of course to implement those common functionalities. At the same time, they use those common functionalities to effect some fine regulation of completely different networks, and therefore there is a relevant part of the functional information conserved in each protein which differs in the two proteins. We are seeing a clear example of modular design, with differentiated functions, which implies the careful selection of long and specific AA sequences, for a total functional complexity of about 1500 bits, well beyond the range of any non design explanation. b) The pattern of differences between SATB1 and SATB2 are fairly easy to explain and I admit I don’t understand why they suggest an irreducibly complex system as you say. An ancestral SATB gene would have duplicated in the vertebrate common ancestor. In each lineage the 2 genes would have accumulated differences starting from that initial divergence. When 2 lineages split from each other the SATB1 and SATB2 genes would then start to accumulate differences from their homolog in the other species. This is a pretty straightforward explanation that explains the pattern. I don’t see how one could explain the same pattern in terms of ID. Everyone can decide for himself how these explanations match the facts. However, I don't think that "the discussion here with RodW is going to go nowhere". It has already been precious, allowing me (and others) to express our arguments, and I really hope that RodW will express further thoughts from his point of view, and I really hope that they will be quality thoughts, because only quality thoughts can really evoke quality answers. :) After all, the purpose is not to convince anyone, but rather to express good ideas about important stuff.gpuccio_{July 15, 2017
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It has been fashionable for those on the ID side to highlight (the critics would say quote-mine) the following quote from Richard Lewontin’s 1997 NYT review of Carl Sagan’s book, The Demon-Haunted World: Science as a Candle in the Dark.
We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.
Indeed, Lewontin is to be commended for his honesty, for being up front about his philosophical biases. On the other hand, he provides absolutely no justification for his philosophical beliefs. Because Richard Lewontin believes something doesn’t make it true for everyone else. He just asserts without argument that scientific explanations based on materialism are for some reason absolute. According to what standard? Indeed, he contradicts the criticism he made just a few paragraphs earlier of his fellow Darwinists.
As to assertions without adequate evidence, the literature of science is filled with them, especially the literature of popular science writing. Carl Sagan’s list of the “best contemporary science-popularizers” includes E.O. Wilson, Lewis Thomas, and Richard Dawkins, each of whom has put unsubstantiated assertions or counterfactual claims at the very center of the stories they have retailed in the market. Wilson’s Sociobiology and On Human Nature rest on the surface of a quaking marsh of unsupported claims about the genetic determination of everything from altruism to xenophobia. Dawkins’s vulgarizations of Darwinism speak of nothing in evolution but an inexorable ascendancy of genes that are selectively superior, while the entire body of technical advance in experimental and theoretical evolutionary genetics of the last fifty years has moved in the direction of emphasizing non-selective forces in evolution. Thomas, in various essays, propagandized for the success of modern scientific medicine in eliminating death from disease, while the unchallenged statistical compilations on mortality show that in Europe and North America infectious diseases, including tuberculosis and diphtheria, had ceased to be major causes of mortality by the first decades of the twentieth century, and that at age seventy the expected further lifetime for a white male has gone up only two years since 1950. Even The Demon-Haunted World itself sometimes takes suspect claims as true when they serve a rhetorical purpose as, for example, statistics on child abuse, or a story about the evolution of a child’s fear of the dark.
I wholeheartedly agree. Just-so stories are never adequate. The honest answer when we don’t know is to honestly admit that we don’t know. With that said, I don’t think that the discussion here with Rob W. is going to go anywhere, because he is going to stick tenaciously to his just-so stories rather than admit that he just doesn’t know. The natural scientific theories need to be built on factually established evidence, not Darwin of the gaps just-so-stories.john_a_designer_{July 15, 2017
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The articles quoted in my last posts fully confirm the role of SATB1 and SATB2 as critical super-regulators. These are obviously very important proteins, at the center of complex networks. They probably bind DNA in a similar way, especially at so called matrix attachment regions (MARs), and induce a local chromatin-loop remodeling. But what happens after the DNA binding, and in what cells and context it happens, is dramatically different for the two molecules. This is the rule for regulatory proteins and, in general, transcription factors. They do bind DNA, but the specificity of their regulatory action is given by the further interactions and bindings with many other complex molecules. TFs often act in macro-complexes that include even 10-15 proteins, or more. And the key to the effect is, very often, a modification of chromatin structure, often generating new loops that bring together distant genes that need to interact, especially enhancers. Are these regulatory systems irreducibly complex? Of course they are. The specificity of the regulation depends critically on the interaction of many complex agents. This kind of system is even more irreducibly complex than a protein cascade, like the famous coagulation cascade quoted by Behe in Darwin's Black Box, because a cascade, although of course irreducibly complex, is in some way a linear connection of enzymatic activities, whose purpose is the amplification and regulation of a process that yields a final product. The regulatory networks we are dealing with here, instead, are complex 3D networks of interactions, with many more dimensions than a "simple" cascade. Chromatin 3D structure is a complex and flexible space of states, that we still understand only marginally. And the states of DNA from the point of view of biophysics are probably even more complex and elusive. We are here in the full domain of epigenetics, which is daily revealing itself as the master controller of all cell processes. With this kind of molecules, we are exactly at the core of the problem, of its mystery and fascination.gpuccio_{July 15, 2017
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SATB1: Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment. (2017) Abstract Most Foxp3+ regulatory T (Treg) cells develop in the thymus as a functionally mature T cell subpopulation specialized for immune suppression. Their cell fate appears to be determined before Foxp3 expression; yet molecular events that prime Foxp3- Treg precursor cells are largely obscure. We found that Treg cell-specific super-enhancers (Treg-SEs), which were associated with Foxp3 and other Treg cell signature genes, began to be activated in Treg precursor cells. T cell-specific deficiency of the genome organizer Satb1 impaired Treg-SE activation and the subsequent expression of Treg signature genes, causing severe autoimmunity due to Treg cell deficiency. These results suggest that Satb1-dependent Treg-SE activation is crucial for Treg cell lineage specification in the thymus and that its perturbation is causative of autoimmune and other immunological diseases. And: SATB1 Plays a Critical Role in Establishment of Immune Tolerance. (2016) Abstract Special AT-rich sequence binding protein 1 (SATB1) is a genome organizer that is expressed by T cells. T cell development is severely impaired in SATB1 null mice; however, because SATB1 null mice die by 3 wk of age, the roles of SATB1 in T cell development have not been well clarified. In this study, we generated and analyzed SATB1 conditional knockout (cKO) mice, in which the SATB1 gene was deleted from all hematopoietic cells. T cell numbers were reduced in these mice, mainly because of a deficiency in positive selection at the CD4(+)CD8(+) double-positive stage during T cell development in the thymus. We also found that SATB1 cKO mice developed autoimmune diseases within 16 wk after birth. In SATB1 cKO mice, the numbers of Foxp3(+) regulatory T (Treg) cells were significantly reduced at 2 wk of age compared with wild-type littermates. Although the numbers gradually increased upon aging, Treg cells in SATB1 cKO mice were still less than those in wild-type littermates at adulthood. Suppressive functions of Treg cells, which play a major role in establishment of peripheral tolerance, were also affected in the absence of SATB1. In addition, negative selection during T cell development in the thymus was severely impaired in SATB1 deficient mice. These results suggest that SATB1 plays an essential role in establishment of immune tolerance. Link: http://www.jimmunol.org/content/196/2/563.full.pdfgpuccio_{July 15, 2017
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SATB2 again: Satb2 Stations Neurons along Reflex Arcs. (2016) Abstract The nociceptive flexor withdrawal reflex has an august place in the history of neuroscience. In this issue of Neuron, Hilde et al. (2016) advance our understanding of this reflex by characterizing the molecular identity and circuit connectivity of component interneurons. They assess how a DNA-binding factor Satb2 controls cell position, molecular identity, pre-and postsynaptic targeting, and function of a population of inhibitory sensory relay interneurons that serve to integrate both proprioceptive and nociceptive afferent information. And: Satb2 Is Required for the Development of a Spinal Exteroceptive Microcircuit that Modulates Limb Position. (2016) Abstract Motor behaviors such as walking or withdrawing the limb from a painful stimulus rely upon integrative multimodal sensory circuitry to generate appropriate muscle activation patterns. Both the cellular components and the molecular mechanisms that instruct the assembly of the spinal sensorimotor system are poorly understood. Here we characterize the connectivity pattern of a sub-population of lamina V inhibitory sensory relay neurons marked during development by the nuclear matrix and DNA binding factor Satb2 (ISR(Satb2)). ISR(Satb2) neurons receive inputs from multiple streams of sensory information and relay their outputs to motor command layers of the spinal cord. Deletion of the Satb2 transcription factor from ISR(Satb2) neurons perturbs their cellular position, molecular profile, and pre- and post-synaptic connectivity. These alterations are accompanied by abnormal limb hyperflexion responses to mechanical and thermal stimuli and during walking. Thus, Satb2 is a genetic determinant that mediates proper circuit development in a core sensory-to-motor spinal network. Satb2 Regulates the Differentiation of Both Callosal and Subcerebral Projection Neurons in the Developing Cerebral Cortex. (2015) Abstract The chromatin-remodeling protein Satb2 plays a role in the generation of distinct subtypes of neocortical pyramidal neurons. Previous studies have shown that Satb2 is required for normal development of callosal projection neurons (CPNs), which fail to extend axons callosally in the absence of Satb2 and instead project subcortically. Here we conditionally delete Satb2 from the developing neocortex and find that neurons in the upper layers adopt some electrophysiological properties characteristic of deep layer neurons, but projections from the superficial layers do not contribute to the aberrant subcortical projections seen in Satb2 mutants. Instead, axons from deep layer CPNs descend subcortically in the absence of Satb2. These data demonstrate distinct developmental roles of Satb2 in regulating the fates of upper and deep layer neurons. Unexpectedly, Satb2 mutant brains also display changes in gene expression by subcerebral projection neurons (SCPNs), accompanied by a failure of corticospinal tract (CST) formation. Altering the timing of Satb2 ablation reveals that SCPNs require an early expression of Satb2 for differentiation and extension of the CST, suggesting that early transient expression of Satb2 in these cells plays an essential role in development. Collectively these data show that Satb2 is required by both CPNs and SCPNs for proper differentiation and axon pathfinding Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585495/pdf/bhu156.pdfgpuccio_{July 15, 2017
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About SATB2: Just to understand what we are dealing with, here: Satb2 determines miRNA expression and long-term memory in the adult central nervous system. (November 2016) Abstract SATB2 is a risk locus for schizophrenia and encodes a DNA-binding protein that regulates higher-order chromatin configuration. In the adult brain Satb2 is almost exclusively expressed in pyramidal neurons of two brain regions important for memory formation, the cerebral cortex and the CA1-hippocampal field. Here we show that Satb2 is required for key hippocampal functions since deletion of Satb2 from the adult mouse forebrain prevents the stabilization of synaptic long-term potentiation and markedly impairs long-term fear and object discrimination memory. At the molecular level, we find that synaptic activity and BDNF up-regulate Satb2, which itself binds to the promoters of coding and non-coding genes. Satb2 controls the hippocampal levels of a large cohort of miRNAs, many of which are implicated in synaptic plasticity and memory formation. Together, our findings demonstrate that Satb2 is critically involved in long-term plasticity processes in the adult forebrain that underlie the consolidation and stabilization of context-linked memory. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5207769/pdf/elife-17361.pdfgpuccio_{July 15, 2017
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Dionisio, do you mean complex, functionally specified information? KFkairosfocus_{July 14, 2017
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gpuccio @ 10-15: Well done! I appreciate RodW's challenging comments seeking understanding and truth. He clearly brings a lot to the table on this topic, and you responded admirably. I am learning a great deal from you both.Truth Will Set You Free_{July 14, 2017
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Dionisio at #22: How true, how true! :)gpuccio_{July 14, 2017
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RodW: I am looking forward to your interventions, and I hope that the discussion will go deeper and deeper. Please, take all the time that is necessary. :)gpuccio_{July 14, 2017
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Let's not forget that gpuccio has given us other long, well written and highly informative articles on this subject of functional specified information "somehow" added to proteins. This time he treats us with another deeply researched article, filled with technical data and analytical commentaries that shed much light on the important subject, while making it easier for the commoner laymen like myself to at least get an idea of the interesting situation that is presented. On top of this gpuccio promises a follow-up article. However, while trying to understand the significance of what is said in this thread, we should keep in mind the clever observation gpuccio wrote @8, which is quoted @20. All the complexity associated with the main idea proposed by gpuccio in his most recent articles --i.e. the inexplicable appearance of functional specified information in the analyzed proteins-- is just the 'antipasti' in relation to what is implied by his comment @8, quoted @20. Let's not be naïve. The deeper science looks into the biological systems, the more obvious the appearance of design is becoming, leading us to the logical realization that it's much more than just appearance. We have no precedence to the marvelous informational systems seen in biology these days. The only things comparable are the sophisticated systems created by many scientists and engineers through cumulative knowledge and experience. Complex functional specified complexity. Whoever runs away from accepting that reality --which is increasingly supported by a growing avalanche of evidences-- is surrendering to a philosophical worldview that is visibly doomed to becoming another shameful page of human history. We ain't seen nothin' yet. The most fascinating discoveries are still ahead. Work in progress... stay tuned.Dionisio_{July 14, 2017
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gpuccio I'll try to write a substantial response in a few hours but I might have to wait till I can get to my work computer on Monday! My home computer is crap!RodW_{July 14, 2017
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Let's repeat something important that gpuccio wrote @8:
"The fascinating thing is that we are still very far from understanding how such regulatory proteins work. I suppose that we still miss a lot about the role of chromatin remodeling, and 3D organization of DNA and RNA."
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Dionisio: "beetles evolved from Liverpool in the UK," That's better than most neo darwinian just so stories :) "Well, RodW helped to heat up the discussion right after the thread started." Yes, he was very kind, given the shortage of discussing opponents. And his arguments were stimulating. :)gpuccio_{July 14, 2017
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Well, RodW helped to heat up the discussion right after the thread started.Dionisio_{July 14, 2017
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gpuccio: beetles evolved from Liverpool in the UK, though were spotted in Germany too, and later had several major random functional mutations: 1. the sequence "The " got added in the front. 2. the 'b' changed to 'B' in the first position 3. an 'e' changed to 'a' (3rd position) The whole change turned positive or advantageous and thus the mutated beetles became much louder The Beatles which were under selective pressure of wildly screaming crowds of teenagers :)Dionisio_{July 14, 2017
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Mung: Of course flies evolved from humans. And beetles? :)gpuccio_{July 14, 2017
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RodW: Well, I have said what I had to say. You will not be convinced, of course. I am well accustomed to that. Just one thing I want to add: I have really appreciated your comments. Indeed, what I really hope for when I publish my OPs, or simply my comments, is that some interlocutor from the other side will give intelligent and reasonable comments. That is the only way ideas can grow, and almost all my best ideas (if there are any) are the result of some passionate confrontation with my patient interlocutors. So, thank you again. :) (Of course, you are welcome to go on with your comments)gpuccio_{July 14, 2017
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RodW:
Its also hard to explain why the pattern of difference would fit the same nested hierarchy build by assuming evolution from anatomy and the fossil record.
Why? I believe in common descent. Designed common descent. I have no problems with nested hierarchies. A lot of human designed artifacts fit in a natural nested hierarchy. What's the problem?
The pattern of differences between SATB1 and SATB2 are fairly easy to explain and I admit I don’t understand why they suggest an irreducibly complex system as you say.
Really? Let's see...
An ancestral SATB gene would have duplicated in the vertebrate common ancestor. In each lineage the 2 genes would have accumulated differences starting from that initial divergence. When 2 lineages split from each other the SATB1 and SATB2 genes would then start to accumulate differences from their homolog in the other species. This is a pretty straightforward explanation that explains the pattern. I don’t see how one could explain the same pattern in terms of ID.
Ah, I was really missing darwinian just so stories. It has been some time since someone offered some here in a discussion! :) So, let's see. We have the original gene in the common ancestor. OK. What's its function? What does it regulate? T cells or neurons? Nobody knows. Nobody will ever know. OK, but it duplicates. So, one of the copies goes on regulating T cells, or what else, and the other copy opts for neurons? No, wait, both copies accumulate differences. Because of neutral evolution, I suppose. So, after a short time, the two copies, in sharks, are a little different. They share only 468 identities, give or take, if we judge from the present proteome. At some point, however, that divergence stops. Those 468 identities remain for the following 400 million years. OK, you will say, we have reached the really functional core of 468 AAs. So, that is conserved. OK, say I, but then why in SATB1, if compared to human SATB1, the functional core which is conserved after 400 million years is of 603 AAs? And the same in SATB2? IOWs, as I have tried to explain in my OP, why is each single protein more conserved than what we see comparing the two proteins, both in humans and in sharks? The answer is simple enough: because the differences between SATB1 and SATB2, both in sharks and in humans, are not due to neutral evolution or divergence: they are functional. That's why the differences are conserved for more than 400 million years, exactly like the similarities. IOWs, SATB1 and SATB2 share 468 AAs, give or take, because they do something in the same way, and are different for other 130 AAS, guve or take, because they do something else which is different. Because those 130 AAs are also functional, because in each protein those different 130 AAs are conserved, too, for more than 44 million years. Can you see my point? This is very easy to explain form a design point of view: the two sister proteins are designed together, as a whole system, probably starting form a similar precursor which is not yet functional. Then each of the two forms is specialized for different tasks, using the common basic sequence for the aspects which are shared in those tasks. That's why I say that it is an irreducibly complex system. There is a common conception, and a very efficient differentiation. A very good design, which has performed well for a very long time. More in next post (the last one, I promise).gpuccio_{July 14, 2017
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RodW:
When one does a protein blast with humans one finds sharks with about 80% but as one gets closer to humans that number increases. The chimp protein is 100% identical. Its hard to explain why this would be the case for domains using ID since presumably the human HOX domain would work just as well in a shark.
You make some important errors here. Of course the homology, even if already high in sharks, continues to increase afterwards, up to the 100% or similar in primates. That is not difficult at all to explain, from an ID point of view. There are two different things that we must consider: a) Domains are not, as you seem to thing, rigid modules that will be always reused in the same way. They need to be adapted to each specific situation. That is true not only of domains, but of every biological structure. Many of the differences between species are obviously due to specific functional adjustments, even when the basic module is reused. A protein can be tweaked for a lot of reasons, like a different cell environment, different interactions, different regulations, and so on. Again, your idea of protein domains and of proteins in general is really rigid and simplistic. b) Neutral evolution happens, I absolutely believe that. That's why I consider conserved sequences as functional only if they are separated by hundreds of millions of years. As I have explained in my previous post, neutral evolution can cancel practically all homologies from sequences that were the same at the beginning, provided that: 1) Those sequences are not functional 2) There is time enough for neutral evolution to happen. We know from the study of synonimous mutations in proteins that 400 million years are more than enough to ensure "saturation", IOWs, that no homology can be detected between synonimous sites after that time. The thing is different, of course, for functionally constrained sites. That's why our 600+ AAs are the same in shark and humans after more than 400 million years. That's why such a conservation is a safe signature of functionality. But when we compare a sequence between humans and chimps, and we find 99% homology, we cannot really say if part of that homology is simply due to the fact that the twi lines diverged only a few million years ago: the time is too short. So, let's say that with short chronological separations, we can expect some amount of "passive" homology, not corresponding to a true functional constraint. That's why I have always used homologies between distant lineages to infer functional constraint.
Its even harder for ID to explain the pattern of differences in the sequence between the domains since its function is to hold the domains together and an astronomically large number of aa sequences should suffice.
Again, the same error, I have already discussed that. It is not true, absolutely not true, that the function of the sequence between the domains is to hold the domains together. Where did you get that strange idea? What are you proposing, that interdomain sequences are junk? :) More in next postgpuccio_{July 14, 2017
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In fact the CUT and HOX domains were discovered first in drosophila and the SATBIN domain is in flies as well.
The obvious conclusion is that flies evolved from humans.Mung_{July 14, 2017
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RodW:
Ecclesiastes 1:9 says “there is nothing new under the sun” This reflects the fact that many of the things we at first think are new are really conglomerations of old things.
I don't want to contradict Ecllesiastes, but do you mean that Shakespeare's sonnets, or Windows 7, are just "conglomerations of old things"? Seriously, are you denying the informational novelty in designed things? Are humans the same thing as LUCA? Are E. coli and a fly the same thing, just "conglomerations of old things"? And the first living cells, were they just "conglomerations of old things"? Of stones and water and what else?
This applies to many of the ‘novel’ proteins in vertebrates which are really just new combinations of old protein domains.
Again, you make a gross error and oversimplification here. First of all, it is not true that there are no new domains in vertebrates. You certainly know that the appearance of new domains goes on throughout all natural history, even if at a constantly decreasing rate. But again, I am not discussing domains here. And do you really believe that a "new combinations of old protein domains" implies no new information? The domains, even when used in different proteins, are never the same. Their sequence changes a lot, and not only for neutral evolution, but also because domains are used differently in different proteins. Some similarity of sequence and structure and function does not mean that we are in front of the same thing. And, of course, the combination of new domains is in itself a huge bulk of new information, new planning, new purpose. Moreover, you seem to believe that all the parts of a protein between detectable domains are simply connections, almost useless. But that is completely wrong: a) We don't know all domains, new ones are detected as our understanding gorws. b) A lot of interdomain sequences are extremely conserved, and certainly functional, as I have shown many times, including in this OP. c) You seem to ignore that a lot of proteins or protein parts are "intrinsically disordered" and lack a recognizable fixed structure, and yet they are very functional just the same. As I have clearly stated in my OP, in SATB1 and SATB2 the interdomain parts of the sequence are extremely conserved too, and therefore almost certainly functionally constrained. You seem to believe that proteins are just a collection of fixed modules in random order. But that is not the case. the connection between sequence and function in proteins is much more complex and in many cases still not well understood, and this is especially true for regulatory proteins, whose functional details still elude us. SAB1 and SATB2 certainly bind to DNA, but that is only the beginning of the story. In your reductionist approach, you seem to stop there.
When we don’t know much about a new structure or protein it can be claimed that it required an infusion of information from an intelligent source. But when we discover how random genomic events could have created this new entity it can be dismissed as not really new.
When we "discover how random genomic events could have created this new entity"????? Are you serious? Examples, please. I have been waiting for years! Just to start, why don'y you offer some thoughts about how "random genomic events could have created", in a few million years, the new sequence of 525 functional AAs that did not exist before, and that was so successful that it was preserved by purifying selection for 400 million years afterwards? More in next post.gpuccio_{July 14, 2017
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RodW: Thank you for your comments. Here are my answers:
While the protein is unique to vertebrates as you say, the domains that allow the protein to perform its function are not. In fact the CUT and HOX domains were discovered first in drosophila and the SATBIN domain is in flies as well. These domains are also part of larger families which perform similar functions.
As seen in Fig. 2, The SATB1_N and CUTL domains are the only two parts of the molecule which have any detectable homology in pre-vertebrates. I have clearly said it in my OP. I have never discussed if those domains are present, in different form, in other pre-vertebrate species. My analysis is based on sequences, and the sequence says that there is no relevant homology before vertebrates except for those that I have clearly mentioned and quantified. This is one of the most common biases of neo-darwinian thought. Those who reason as you are doing here are satisfied to detect any vague link between proteins in different species, sometimes only of structure, not even sequence, to rejoice and be sure that all is explained. But that is simply not true. ASome vague connection (which can certainly be present in many cases) does not explain the following jumps in information. Remember, I am not arguing that there is no contiuity in the proteome. I do believe that there is. I do believe in common descent, and indeed all my arguments are based on common descent. But common descent does not explain in any way the appearance of new huge amounts of functional information. Maybe you are missing the main point in my argument. I will try to be more clear. Human and sharks share in SATB1, after more than 400 million years, a conserved sequence of about 525 AAs (603-78) that was not at all detectable in all older species. These are functionally constrained AAS, because they are conserved for 400 million years. This specific sequence did not exist before. Can I be more clear than this? It's not important if the domains, in different form, have been in some way identified before. I am not discussing the individual domains. I am discussing the functional sequence, because evolution through supposed RV happens in the space of sequences. More in next post.gpuccio_{July 14, 2017
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Thanks for the post. Its obvious you've put a lot of work into it. I disagree that this shows evidence for ID. While the protein is unique to vertebrates as you say, the domains that allow the protein to perform its function are not. In fact the CUT and HOX domains were discovered first in drosophila and the SATBIN domain is in flies as well. These domains are also part of larger families which perform similar functions. Ecclesiastes 1:9 says "there is nothing new under the sun" This reflects the fact that many of the things we at first think are new are really conglomerations of old things. This applies to many of the 'novel' proteins in vertebrates which are really just new combinations of old protein domains. This provides a good debating tactic for IDers. When we don't know much about a new structure or protein it can be claimed that it required an infusion of information from an intelligent source. But when we discover how random genomic events could have created this new entity it can be dismissed as not really new. When one does a protein blast with humans one finds sharks with about 80% but as one gets closer to humans that number increases. The chimp protein is 100% identical. Its hard to explain why this would be the case for domains using ID since presumably the human HOX domain would work just as well in a shark. Its even harder for ID to explain the pattern of differences in the sequence between the domains since its function is to hold the domains together and an astronomically large number of aa sequences should suffice. Its also hard to explain why the pattern of difference would fit the same nested hierarchy build by assuming evolution from anatomy and the fossil record. The pattern of differences between SATB1 and SATB2 are fairly easy to explain and I admit I don't understand why they suggest an irreducibly complex system as you say. An ancestral SATB gene would have duplicated in the vertebrate common ancestor. In each lineage the 2 genes would have accumulated differences starting from that initial divergence. When 2 lineages split from each other the SATB1 and SATB2 genes would then start to accumulate differences from their homolog in the other species. This is a pretty straightforward explanation that explains the pattern. I don't see how one could explain the same pattern in terms of ID.RodW_{July 14, 2017
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Dionisio: "Making the amazing bacteria flagellum look like a Lego toy for toddlers." Indeed. :) The fascinating thing is that we are still very far from understanding how such regulatory proteins work. I suppose that we still miss a lot about the role of chromatin remodeling, and 3D organization of DNA and RNA. I have found very interesting the video from AmNat by Sal Cordova posted by johhnyb, that deals with some of these aspects.gpuccio_{July 14, 2017
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"The whole system is certainly much more irreducibly complex than we can imagine." Making the amazing bacteria flagellum look like a Lego toy for toddlers. :)Dionisio_{July 14, 2017
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A ton of information in this article for readers to process. I still haven't chewed and digested the whole article. It's heavily loaded with important information, literally causing a "Big Data" problem here. :) Let's see how the discussion goes. Here's science at its best. No reason for the politely dissenting interlocutors to whine again. Just come and discuss. Put aside the philosophical issues.Dionisio_{July 14, 2017
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DNA-binding protein SATB1

Evolutionary history of SATB1

Fig. 1: Evolutionary history of SATB1 by human-conserved functional information

Fig. 2: Results of blasting human SATB1 against all non vertebrate protein sequences

Fig. 3: The best hit in non vertebrates (with a spider)

The information jump in vertebrates

Fig. 4: The best hit of human SATB1 in cartilaginous fish (with the whale shark)

Functionality

DNA-binding protein SATB2

Fig. 5: Blast of human SATB1 vs human SATB2:

Fig. 6: Evolutionary history of SATB2 by human-conserved functional information

Fig. 7: Evolutionary history of SATB1 and SATB2 by human-conserved functional information

Fig. 8: The best hit of human SATB2 in cartilaginous fish (with the whale shark)

Fig. 9: Blast of whale shark SATB1 vs whale shark SATB2:

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