One of the primary arguments against evolution is that many things about life are too complicated to have evolved by chance. The argument is that these tiny molecular machines are so complex, and so exquisitely intricate and precise, that they could not function if any of the components were missing, damaged, or less complex. This idea was published in 1996 by Michael Behe, a biochemist. Shouldn’t he know?
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.– Behe, M. 1996. Darwin’s Black Box: The Biochemical Challenge to Evolution. Simon & Schuster Inc.
One of the primary examples of an “irreducibly complex” machine is a flagella. It is argued that, if any components of the flagella were missing, the flagella would not, and could not, function. This argument persists.
A flagella IS complex! However, it is important to remember that are different types of flagella, different constructions. It may help to think of them like cars: there are different styles; some have 4-cylinder engines, some have carburetors (remember those?).
An article that is soon-to-be published deals with how increasing complexity can evolve.
This article deals with a machine that is far more complex, and FAR more integral for life than a flagella: the ATPase proton pump. For those new to such things, ATP is adenosine triphosphate, the main form of cellular energy. The ending -ase indicates an enzyme. Therefore, this is an enzyme that makes ATP (cellular energy), and it does so by pumping protons (H+). This piece of equipment or machinery is fundamentally critical for complex life: we need it to convert food (glucose) to pure energy and power EVERYTHING else in our cells.
What is it and how does it work?
For now, just pay attention to part (a) of their Figure 1. This pump has a flower-like head and a ring structure that each have 6 subunits (that’s called a hexamer). This pump has a ratchet-like action. When it rotates, it pushes a proton (H+) through a membrane. This produces something like an electrical current that is used to make ATP. In particular, the researchers focused on the bottom V0 ring (colored) of this assembly.
The individual pieces that make up this ring are different in different types of critters:
In animals and most other eukaryotes, the ring consists of one subunit of Vma16 protein and five copies of its paralogue, Vma3 (Fig. 1b)1. In Fungi, the ring consists of one Vma16 subunit, four copies of Vma3 and one Vma11 subunit, arranged in a specific orientation17. All three proteins are required for V-ATPase function in Fungi18,19, but the mechanisms are unknown by which both Vma3 and Vma11 became obligate components with specific positional roles in the complex.
What that says is that fungi need 3 different TYPES of proteins to make that ring work properly. Animals need 2 types. How exactly those proteins get assembled seems to matter as well.
What did they do?
They started with genetics. Thornton’s team took 139 versions of these proteins (Vma3, Vma11, Vma16) and compared them. Computer software was used to figure out a gene sequence (DNA) that would be the MOST similar to ALL 139 versions. This should be the “ancestral” protein. Next, they chemically made this gene in a lab (yeah, we can do that). During this, they found out that Vma3 and Vma11 are actually extremely similar–like sisters. These two proteins had the same ancestor (like you and your sister had the same mother). They put this gene into yeast whose own genes were screwed up/broken to see whether the ancestral version (Anc.) actually worked. Some yeast were missing the Vma3 gene, some were missing Vma11, and some were missing both. They created Anc.3, Anc.11, Anc.16, and Anc.3-11 (the common ancestor to both sisters). They used extra calcium chloride (CaCl2), which worked kind of like a poison here: if the ancestral proteins worked, the yeast lived; if not, the yeast died.
So did it work?
For yeast missing Vma3: Yes. Replacing Vma3 with Anc.3 worked fine: a lot more yeast survived the CaCl2, almost like normal yeast. Replacing Vma3 with the ancestral Anc.3-11 also worked–just as well as Anc.3! However, replacing the gene with Anc.11 didn’t work at all, so Vma11 cannot replace Vma3.
For yeast missing Vma11: Replacing Vma11 with Anc.11 worked fine, too. Using the Anc.3-11 wasn’t anywhere near as effective, though: only about 25% of the cultures survived. Also, when they tried to replace Vma11 with Anc.3, it failed: no yeast grew. So, Vma3 cannot replace Vma11 either.
So far, we’ve learned that Vma3 and Vma11 are NOT interchangeable with each other, but the common ancestor to BOTH was partially functional (25%). What I’d really like to see is that Anc.3-11 can save yeast that are missing BOTH Vma3 AND Vma11… and it does!!! About 25%!!! Now we know that one ancestral protein probably became modified into two distinct proteins. It originally didn’t work as well as either modern version in existence today, but it did work! This data shows that “we” went from 1 ancestral, semi-effective protein to TWO similar proteins, each of which work better than the original, but that aren’t interchangeable! That is considerably MORE COMPLEX.
What about the third protein, Vma16? It can be replaced with Anc.16 with no apparent loss of function. Maybe 16 hasn’t changed much. If the yeast were missing Vma3, Vma11, AND Vma16, researchers had to give back Anc.3-11 AND Anc.16 to get fully normal growing yeast. So, Vma16 is really different.
One last observation from their data. If they knocked out both Vma3 AND Vma11, they got about a 25% rescue from Anc.3 OR Anc.3-11. Both worked similarly, but not well. To get full rescue, they HAD to use BOTH Anc.3 and Anc.11 separately. So those two proteins are newer, more recent, more modern than Anc.3-11. That is also supported by the observations that 3 could not replace 11 and vice versa.
What does it tell us?
Somewhere in time, Anc.3-11 got copied at least once. One copy became Anc.3, and the other became Anc.11. These went their separate ways to become modern Vma3 and Vma11 that we see today. I made a picture to help.
This paper is a prime example of evolution. Finnigan and his colleagues were able to show that one mathematically predicted ancestral gene worked in place of either modern variant, but not as effectively. Therefore, this system has become both MORE complex and MORE efficient!