The Decline Effect

Remember my concern about naïve realism?

Naïve realism is the conviction that one sees the world as it is and that when people don’t see it in a similar way, it is they that do not see the world for what it is. Ross characterized naïve realism as “a dangerous but unavoidable conviction about perception and reality”. The danger of naïve realism is that while humans are good in recognizing that other people and their opinions have been shaped and influenced by their life experiences and particular dogmas, we are far less adept at recognizing the influence our own experiences and dogmas have on ourselves and opinions. We fail to recognize the bias in ourselves that we are so good in picking out in others.

Of course, many people might be tempted to dismiss this as being rather insignificant, given that science has provided a means to “see the world for what it is.”  Not so fast.  I encourage you to read Jonah Lehrer’s article, The Truth Wears Off : Is there something wrong with the scientific method?

Lehrer explains the Decline Effect, where scientific findings are reported and with time, it becomes harder and harder for others to replicate the findings.  The problem is widespread and there appear to be many factors that bring about this phenomenon. For those who have heard me talk about confirmation bias in the past, you might enjoy this example:

2010 Top Ten: Designing Evolution

I decided to list my top 10 favorite entries from 2010.  By looking back, it helps to confirm my suspicion that the hypothesis of front-loading/nudging evolution is not only reasonable and plausible (as no one has ever shown otherwise), but it is also a fruitful and productive hypothesis.  The ten entries are not ordered by any criteria, but instead roughly follow a chronological sequence.

So here they are……

Nudging beta catenins to emerge

In the previous posting (which was originally posted over a year ago), I was able to track down some papers which uncovered evidence for the existence of various adherens junctions proteins in unicellular organisms. Well, a few days ago, I had the time to probe databases with sequence from human genes in search of homologs for adherens junction proteins in unicellular organisms.

Recall the basic components of an adherens junction as seen in the below figure:

As you can see, the cadherin is the membrane protein used to link cells together. The cadherin, in turn, is linked to the cytoskeletal microfilaments through a complex composed of beta-catenin, alpha-catenin, alpha-actinin, and vinculin.

Below is a table that lists what I found.

The eukaryotic cell: Preadapted for multicellular existence

First, a review.

We’re looking at two different eukaryotic proteins: beta catenin and alpha importin. Beta catenin plays two different crucial roles in metazoan life: 1) It is a key component of the adherens junction which connects cells together and 2) it is involved in the transcription of genes that play an important role in the development of the embryo and the maintenance of organs. This is a neat example of one protein playing two important roles in metazoan life. A simplified figure is shown below, where the beta catenin is represented by the pink circle:

Next are the alpha importins. They transport proteins into the nucleus through the nuclear pore complex. The figure below shows the basic mechanism involved:

The alpha importin is shown in blue. It recognizes and binds the nuclear localization signal (NLS) on a protein that is destined for the nucleus (in the above figure, it is the experimentally designed radioactive protein) and then binds with another protein, beta importin, to be transported into the nucleus.

It is my hypothesis that the alpha importins imposed a form of guidance to evolution by front-loading the eventual emergence of the beta catenins which would, in turn, facilitate the evolution of metazoa. The first line of support for this hypothesis would be to show a homologous relationship between these two different proteins (and as far as I have been able to tell, no one has seriously proposed this). So allow me to make that case.

Three Against One

Nuclear Pore Complex

Click on the image to see some more neat pics

Cousins

In the last entry, we saw that beta catenins and alpha importins appear to have a strikingly similar domain organization as seen by the CDD representations.  So what do the two proteins actually look like?

Another deep, homologous relationship

I have previously tried to show you that it is quite plausible to propose that a protein essential in two multicellular processes existed in the last common ancestor of all eukaryotes. Thus, this could be one front-loaded feature to these cells that would, sooner or later, help to nudge animal life into existence.  But if it is too difficult to believe that something like beta-catenin is as old as the eukaryotic cell itself, let me make it even more clear that beta-catenin was always in the cards.  How?  By showing you that even if beta-catenin is not quite as ancient as I propose, its very existence was front-loaded by the existence of a remarkably similar homolog – alpha importins.

Shadow Life Sensationalism

You have probably heard this story by now:

But now researchers have discovered a bacterium that appears to have replaced that life-enabling phosphorus with its toxic cousin arsenic, raising new and provocative questions about the origins and nature of life.

News of the discovery caused a scientific commotion this week, including calls to NASA from the White House asking whether a second line of earthly life has been found.

Whether or not the bacteria actually replace phosphorus with arsenic is something that will eventually be sorted out.  But for now, we can be confident that no “second line of earthly life has been found.”

“This is different from anything we’ve seen before,” said Mary Voytek, senior scientist for NASA’s program in astrobiology, the arm of the agency involved specifically in the search for life beyond Earth and for how life began here.

“These bugs haven’t just replaced one useful element with another; they have the arsenic in the basic building blocks of their makeup,” she said. “We don’t know if the arsenic replaced phosphorus or if it was there from the very beginning – in which case it would strongly suggest the existence of a shadow biosphere.”

Yes, we do know it wasn’t there from the beginning.  How?

Aardvark

One of the organisms that has a homlog to the Volvox version of beta-catenin is Dictylostium, otherwise known as a slime mold. This organism normally exists as single-celled amoeba, but when stressed, the cells seek each other out to form a multicellular state that looks like a slug, where all cells coordinate with each other for motility and reproductive purposes.

Below is a figure of the lifecycle of this organism:

As you can see, this organism can exist in an amoeboid state, a flagellated state, a multicellular state that mimics slugs and fungi, and as a spore. It even undergoes meiosis. All that biotic diversity packed into a single genome.

Here is a nice video that allows you to see this creature in action:

As mentioned before, the homologs to the Volvox version of beta-catenin are mostly annotated as hypothetical proteins because they were identified from DNA sequence rather than biochemical or genetic screens. Not so with Dictylostium. Its homolog is known. And has been studied. It’s called aardvark.