Monthly Archives: February 2012

Biological History: Strickland on Zoological Systematics

In looking at the Wallace biogeography flap, I came across an interesting passage in Wallace’s 1855 Sarawak paper:

We shall thus find ourselves obliged to reject all those systems of classification which arrange species or groups in circles, as well as those which fix a definite number for the divisions of each group. The latter class have been very generally rejected by naturalists, as contrary to nature, notwithstanding the ability with which they have been advocated; but the circular system of affinities seems to have obtained a deeper hold, many eminent naturalists having to some extent adopted it. We have, however, never been able to find a case in which the circle has been closed by a direct and close affinity. In most cases a palpable analogy has been substituted, in others the affinity is very obscure or altogether doubtful. The complicated branching of the lines of affinities in extensive groups must also afford great [[p. 188]] facilities for giving a show of probability to any such purely artificial arrangements. Their death-blow was given by the admirable paper of the lamented Mr. Strickland, published in the ‘Annals of Natural History,’ in which he so clearly showed the true synthetical method of discovering the Natural System.

Hmmm, OK. What are the odds that one could manage to lay hands on a paper published about 172 years ago? Google search for “Annals of Natural History Strickland” placed an Internet Archive link high in the ranking. That page offers the text of the paper in several different formats.

So what does Mr. Strickland say about systematic work?

The postulate with which I commence the inquiry is, to let
it be granted that there are such things as species, distinct in their characters and permanent in their duration. This being admitted, we define the natural system to be the arrangement of species according to the degree of resemblance in their essential characters. In other words, the natural system is that arrangement in which the distance from each species to every other is in exact proportion to the degree in which the essential characters of the respective species agree. Hence it follows that the whole difficulty of discovering the natural system consists in forming a right estimate of these degrees of resemblance. For the degree in which one species resembles another must not be estimated merely by the conspicuousness or numerical amount of the points of agreement, but also by the physiological importance of these characters to the existence of the species. On this point no certain rules have yet been laid down ; for though naturalists in general admit, for instance, that the nervous system is superior in importance to the circulatory, and the latter superior to the digestive system, yet this subject is still in a very indeterminate state, and until our knowledge of physiology is much further advanced, disputes will always arise respecting the true position of certain species in the natural classification. Such differences of opinion, however, will continually diminish as our knowledge increases, and they are even now very few in comparison with the numerous facts in classification on which all naturalists are agreed. Much may be effected by education and habit, which impart to the naturalist a peculiar faculty (termed by Linnaeus a ” latent instinct 5 ‘) for appreciating the relative importance of physiological characters to the satisfaction of himself and others, even in cases where he is unable to explain the principles which determine his decision.

Strickland devotes the bulk of his paper, though, to a thorough trashing approaches to systematics that proposes some ordering principle from without. Linear arrangements, numerological arrangements, and circular arrangements all come in for deconstruction and dismissal.

The best part I see, though, is Strickland’s argument for why variety is and must be the aspect of nature that zoologists simply have to accede to.

2. It follows from the irregularity of external nature, as seen on the surface of the earth, that the groups of organized beings must be irregular also, both in their magnitudes and in their affinities. In proof of this it must be granted that the final cause of the creation of every animal and plant is the discharge of a certain definite function in nature, and not the mere occupation of a certain post in the classification : in short, that the design of creation was to form not a cabinet of curiosities, but a living world. Few, I trust, would hesitate to admit this proposition. If, then, the different modifications of structure which constitute the characters of groups were given solely with reference to the external circumstances in which the creature is destined to live, it follows that the irregularities of the external world must be impressed upon the groups of animals and of plants which inhabit it. The supply of organic beings is exactly proportioned to the demand ; and Nature does not, for the sake of producing a regular classification, go out of her way to create beings where they are not wanted, or where they could not subsist. Thus, for instance, the warm climate and varied soil of the tropics admits of the growth of a vast variety of flowers and fruits. The group of Humming-birds which feed on the former, and of Parrots which feed on the latter, are accordingly found to be developed in a vast variety of generic and specific forms ; while the family of Gulls which seek their food in the monotonous and thinly inhabited regions of the north, are few in species and still fewer in genera. Again, the variety of plants in the tropics admits the existence of a great variety of insects, and the family of woodpeckers is proportionately numerous; while the Oxpecker {Buphaga) % which seems to form a group fully equivalent in value to the Woodpeckers, is limited to but one or two species, because its food is confined to a few species of insects which only infest the backs of oxen.

It follows, then, that the groups of organized beings will be great or small, and the series of affinities will be broken or
continuous, solely as the variations of external circumstances
admit of their existence, and not according to any rule of
classification. If, indeed, we were to imagine a world laid
out with the regularity of a Chinese garden, in which a certain number of islands agreeing in size, shape, soil, and form of surface, were placed at exactly equal distances on both sides of the equator, we might then conceive the possibility of a perfect symmetry in the groups of beings which inhabit them ; but without some such supposition, I do not see how a class of animals or plants can be symmetrical in themselves, and yet be expressly adapted for conditions of existence which are eminently irregular.

This statement of Strickland’s appears to express the concept of niche that Joseph Grinnell would be credited with some sixty-seven years later in 1917. There is the persistent difficulty in looking at almost all Victorian-era naturalist writings pre-Origin-of-Species that everything has to be couched in terms of some sort of creationary framework. But the citation of Strickland in Wallace’s 1855 paper does show a nice progression in the history of ideas, where a concept of dependence of a species on a set of environmental conditions leads to the concept of biogeography relating species not just to particular constraints, but also to particulars of place and time in relation to parent and daughter species.

The particular proposal of Strickland’s, to evaluate characters weighted in some way by importance to the species in order to assess affinities to other species, markedly differs from what is considered current today. The cladistic approach developed in the 1960s explicitly gets rid of “weighting” schemes and the notion that a few well-understood characters are better for assessing affinity than many characters simply noted as present or absent. So Strickland’s actual proposal of what the true method of discovering the natural system would be hasn’t held up, but several of his reasons for rejecting prior methods still carry weight, and his expression of this appears to have contributed to the development of biogeography as a topic.

Coyne, Wallace, and Flannery

There’s a post on “PRUnderground” that takes delight in an alleged screwup by Prof. Jerry Coyne. Coyne is stated to have made a claim during a radio program about Alfred Russel Wallace:

In particular, Jerry was emphatic in claiming Alfred Russel Wallace never connected biogeography to evolution: “Wallace did not use biogeography as evidence of evolution. I mean, never!”

Given that “intelligent design” comes into it later, I’m suspicious about the veracity of any such quote. It certainly is a staple of religious antievolution argument to get things wrong. So I’ll note that the basis for everything else is not verified and go on with the assumption that the author did manage to convey that claim of Coyne’s in essence.

The article then goes on to discuss Coyne’s claim, or, rather, to claim to discuss Coyne’s claim:

That’s not how I remember this history, so I decided to check with Wallace biographer Professor Michael Flannery.

Professor Flannery: Well, he seems to really be unfamiliar with Wallace’s body of writing on that topic. The famous paleontologist and geologist, Henry Fairfield Osborn, he’s sort of an icon in the field, referred to Wallace’s Sarawak Law Paper as “A very strong argument for the Theory of Descent and a bold declaration from a strong and fearless Evolutionist.”

And actually if you’d like sort of an icing on the cake reference, Ian McCalman, who has written a pretty good book recently called Darwin’s Armada, refers to Wallace’s Sarawak Law paper as, “The first ever British scientific paper to claim that animals had descended from a common ancestor and then produced closely similar variations which have evolved into distinct species.”

What’s remarkable about this is that the rebutting expert never directly addresses the question at issue. Did Wallace use biogeography to inform his discussion of evolution? Unless you already knew the answer to that, Flannery’s response doesn’t approach it at all. Rebutting Coyne’s claim requires three elements to be shown: Wallace as source, evolution as topic, and biogeography as evidence. The Osborn and McCalman quotes address only the first two of these, leaving the critical component, biogeography, out entirely.

Flannery does mention in passing Wallace’s Sarawak paper. Even a brief skim of the paper is enough to disabuse anyone of the notion that Wallace never used biogeography as evidence of evolution. But one would have to already know the content of the paper in order to decide whether Flannery’s assertion carried weight or not. For completeness, though, I’ll quote Wallace discussing that iconic example, the Galapagos Islands:

Such phænomena as are exhibited by the Galapagos Islands, which contain little groups of plants and animals peculiar to themselves, but most nearly allied to those of South America, have not hitherto received any, even a conjectural explanation. The Galapagos are a volcanic group of high antiquity, and have probably never been more closely connected with the continent than they are at present. They must have been first peopled, like other newly-formed islands, by the action of winds and currents, and at a period sufficiently remote to have had the original species die out, and the modified prototypes only remain. In the same way we can account for the separate islands having each their peculiar species, either on the supposition that the same original emigration peopled the whole of the islands with the same species from which differently modified prototypes were created, or that the islands were successively peopled from each other, but that new species have been created in each on the plan of the pre-existing ones. St. Helena is a similar case of a very ancient island having obtained an entirely peculiar, though limited, flora. On the other hand, no example is known of an island which can be proved geologically to be of very recent origin (late in the Tertiary, for instance), and yet possesses generic or family groups, or even many species peculiar to itself.

Back to the PRUnderground article…

Then, for nausea’s sake, the folks go off into speculation and “intelligent design” cheerleading:

Alex Tsakiris: All this might seem like a lot of minor detail that no one cares about, but this little bit of history is actually quite important in the culture war debate over the theory of evolution. Why does an otherwise smart guy like Dr. Jerry Coyne say these things which are so obviously incorrect? What’s the real agenda here?

Professor Flannery: Well, my guess is that he is either just unfamiliar with Wallace’s work, although that’s kind of hard to believe… I actually think that it just doesn’t serve his purpose. When you look at his book, Why Evolution is True, one of the things he’s writing against is Intelligent Design. To bring Wallace into the picture becomes problematic for him because Wallace himself came to view evolution as being guided.


Here’s the response I entered in comments there:

Coyne was wrong about Wallace. Wallace was wrong about the concept of “intelligent design”. Coyne not completely grasping the history of ideas isn’t helpful, but it in no way can be taken as supporting IDC.

Professor Flannery also doesn’t do well in forming his answer to the question of whether Coyne was right in his claim. Flannery’s first try, invoking Osborn on Wallace’s status as an evolutionist, doesn’t even address the question. For the second, one has to oneself know the content of the Sarawak paper to know that the claim by Coyne is false; it isn’t evident by the statement that Flannery makes. The quote he gives is remarkable for the complete absence of any geographical or biogeographical component.

Update: At Troy Britain’s prompting, I’ve had a look at the Skeptico transcript of the Coyne interview and listened to the segment in the MP3 including the quote from Coyne that was at issue. The quote does fail to give the gist of Coyne’s original claim. That claim is that it was Darwin who was the first to use biogeography as evidence of evolutionary change. Coyne rejects any discussion made by Wallace of both biogeography and evolution that occurs after 1859 as not being relevant to his claim. That makes Coyne’s statement that Wallace “never” used biogeography as evidence for evolution a bit of hyperbole on his part, since his only interest seems to be in who got there first, Darwin or Wallace. Unfortunately, Coyne is mistaken on this point: the 1855 “Sarawak” paper by Wallace is quite explicit in using biogeography to undermine the idea that species are fixed. In 1855, Wallace did not have and did not produce a mechanism for speciation, but it is clear that he was talking about evolution and that he was using biogeography as evidence for it.

Giving Wallace appropriate credit for his innovations is not a concession to religious antievolutionists. Like I said before, Wallace was wrong in his advocacy of stuff that the “intelligent design” creationists have glommed onto. That doesn’t make the good stuff that Wallace did less worthy of notice.

Losing Revenue?

Have a look at this article on the BBC site.

There’s just so much wrong. The mobile telephony companies are toting up projections of profit from SMS and MMS messaging and seeing a shortfall as a “loss”.

“I think it’s a growing threat which is manageable through the right tariffs and the right costing,” Mr Barford added.

“People are still using the mobile networks to communicate – and they’re willing to pay for that.”

Yes, people are wiling to pay to communicate, but they are also going to look to find the best available methods. That evaluation is going to include cost. And the pricing telcos have artificially placed on SMS and MMS messaging simply is uncompetitive with other technologies now.

The buggy-whip manufacturers experienced a “loss of revenue” with the advent of the automobile. That doesn’t mean they deserved to continue getting it, no matter what “tariffs and right costing” they might have contemplated. The only difference here is that the buggy-whip manufacturers were not also the only people selling and servicing automobiles.

Some Data Analysis and Visualization

As noted here before, I’m working through refreshing archived data, mostly from CD-ROM media. I’ve run into a whole batch of CD-ROM disks that are in good physical condition, but which mostly cannot be read. I’m trying some tools that I’ve seen recommended, but would be open to suggestions.

But the whole point of getting the archived data refreshed is to do something with it. And that’s what I will aim to discuss here this time.

Over several years, there were a number of different technologies I was using to collect bioacoustic data. This means that I don’t have one single type of data of interest. I have data that was recorded on audio cassette tape. I have data from a Racal Store V data recorder that was transferred to cassette tape. I have digital data from Keithley-Metrabyte DAS-1800 DAQ, Tucker Davis Technologies DAQ, and a couple of different National Instruments DAQ boards multiplied by at least two different multichannel scenarios. Plus, there’s digital data transferred off of a Racal Storeplex unit via SCSI. There’s mixed endian byte order issues, among other things.

I have a good software solution for two of these particular data acquisition scenarios. I wrote that between 1999 and 2001 using Borland’s Delphi 5. In all, there’s about 60,000 lines of code for data acquisition, reduction, analysis, and visualization. The original can handle multi-channel recordings taken from a single National Instruments board. A variant works on digitized audio recordings. That includes interactive data reduction with an automated click-picker whose choices can be refined with changes in parameters or by interaction with an oscillogram graph.

That still leaves a lot of data waiting for analysis. During my time at Michigan State University, I got into Python programming. There are a number of nice things about going after the rest of the data with Python. A big one is that Python is free, open-source software. I can have colleagues install it and not have to worry about breaking their budgets, which is a concern when one considers the well-established science and engineering scripting platform, MATLAB. While Python doesn’t yet have all the “toolbox” capability of MATLAB, it has enough to move ahead with. For the scientific programmer, there are the Numpy, Scipy, and Pylab modules (I installed the Python(x,y) package on my Windows laptop, which includes those and more besides.) Numpy extends Python with a fast array and matrix manipulation capability. Scipy includes a variety of analysis tools. Pylab looks to put a wrapper on those two, plus the Matplotlib graphics module and the Ipython interactive shell.

I recently wanted to extract spectral information about dolphin clicks from one of the datasets that I hadn’t previously examined. So I turned to Python to do that. The data was stored as raw binary, 16 bit signed integer samples. Reading that data was simply:

fd = open(fn, ‘rb’)
read_data = np.fromfile(file=fd, dtype=np.int16)

where “fn” is a filename pulled from the directory of interest. The “np” reference above resolves to “numpy”. The three lines say to get an open file object, fd, by opening a file, fn, for binary read. Then, a Numpy array containing the data is returned by the Numpy static method, fromfile, given the file object and the specification of the data type as signed 16 bit integers. The third line closes the file object. If I had a problem with endian issues, there’s at least a couple of ways to address that in Numpy. (Getting the wrong byte order should be obvious on visualization, but I’ve seen a professor merrily tout a new processing method for dolphin clicks when his slides clearly showed that he had a byte-order problem with his dataset.)

While it is better to handle DC offset problems at the time of data collection, sometimes you just have to deal with it at analysis time. This dataset handed me that problem. This problem is one where a time-varying signal should be centered at zero volts input, but instead centers at some non-zero voltage. Fortunately, it was a fixed offset, so a pretty simple approach worked nicely: find the mean value across the dataset, and subtract that value from each sample.

shiftdata = read_data + ([-np.average(read_data)])

The use of a Numpy array for the data means that the one line above handles the element-wise addition operation. The Numpy array on the left is now a floating-point array instead of an integer array.

My Delphi program had a click-picking algorithm that took a while to craft. I haven’t ported it yet, so I just went with a very simple approach in Python. That looks at chunks of the data, where the chunksize was selected to be a bit larger than the maximum click width, but a good deal smaller than the interval between clicks. Within each chunk, the maximum value and minimum value are found. If the maximum and minimum are outside a defined noise level, consider it a found feature.

chunkmin = np.min(cary)
chunkmax = np.max(cary)
if (chunkmin < -noiseband) and (chunkmax > noiseband):
# Found a click! Or a transient, at least.
chunkmaxloc = cary.argmax()

Using the Numpy routines to find the min, max, and max location is pretty snappy.

Then, for each “click” located, I ran an FFT to get a power spectral density, and plotted that. I just used example code to add this functionality. (For underwater acoustics where pressure is measured, though, the conversion to decibels uses a factor of 20 rather than 10.)

So, for a quick and dirty script of less than three hundred lines total, I was able to:

* get a directory listing
* match to filename features to identify files to analyze
* remove DC offsets
* save new versions of the data
* scale the data according to field notes
* locate “clicks” in the data
* generate a PSD for each “click”
* collect PSD data
* generate and save oscillogram/PSD plots
* rank “clicks” on spectral features
* copy off plots of the highest-ranked clicks to a directory

My 2.4GHz dual-core Ubuntu workstation ran this script on 230 megabytes of data, producing over 1,400 graphs, and did it in eight minutes time. I’ve just located a calibration sheet on the hydrophone used, so once I’ve digitized that and applied it, I’ll post an example with real dB numbers on the axis.

The Weekend

I don’t know what other people got up to this weekend, but mine has been pretty well filled with computing projects.

I’ve been working with my friend Marc to try to get to the bottom of the Verizon FIOS connection foul-up. We each ran TCPDUMP on our respective machines while making a request that could be fulfilled (a small static HTML page) and one that could not be fulfilled (a dynamic page for webmail). We’ve sent the logs off to a networking guru friend of ours to see if he has any ideas. While I fully expect that this is a problem in Verizon’s gear and processes, we are continuing to test any possibility that a fault in our gear could be an issue.

As I’ve mentioned previously here, I have data stretching back to the mid-1990s on CD-ROM. I’ve made a chunk of progress toward refreshing the archive by copying various of those to hard disk. It takes time, and needs manual attention every five minutes or so to unmount the last disk, load the new disk, mount it, and set up a copy process. Fortunately, most of the disks simply copy without error. I’m using ddrescue to go after the few files that won’t copy cleanly.

I’ve also been going through some of the packed boxes to locate more disks to be refreshed. Along the way, I’ve been reminded that I also have a pile of video and acoustic recordings on tape to digitize as well. I do have a cassette tape deck set up to digitize to my laptop, but I haven’t gotten my desk set up nicely to incorporate the video digitizing machine into a smooth workflow. From left to right, I have a Macbook Pro, a Viewsonic 24″ LED monitor for a second screen for a laptop, a Gateway MT6458 laptop running Win7, an Optiquest 15″ monitor for a desktop machine, plus keyboard and mouse for a desktop. Under the desk itself, I’ve got the video digitizing machine and the workstation/file server box. The video digitizing machine was built as state-of-the-art in 2001. It runs Windows XP, since the digitizing card doesn’t work under anything more recent. It still does a nice job of pulling in analog sources in a DV video stream. The file server is much more recent, being built in 2007. It runs Ubuntu Linux 11.10. There’s 4 terabytes of hard disk storage in that machine, which we use for our project files, personal files, multimedia, photos, and data. We’re coming up to the limits on that, especially after this weekend’s work.

I found a box of pocket notebooks, several of which have notes from our research data collection. But I did find one that has notes from the 1997 Discovery Institute conference on “Naturalism, Theism, and the Scientific Enterprise”. I see from my notes that Michael Ruse classed approaches to “religion v. science” into “conflict”, “accommodation”, and “separation”. I don’t think “accommodation” was used by Ruse in exactly the same way that more recent commentary has gone, but I thought it interesting to see the word there, anyway.

I’m also working on some Python programming and a PHP/MySQL project. Between these things, that pretty well soaks up the time.

Critical Analysis, Critically Analyzed

Dr. Eugenie Scott is giving a public talk Thursday, February 9, 2012, at the University of South Florida in Tampa. The topic is on the “critical analysis” legislative efforts that have popped up in Florida, and how these are part and parcel of the creationism movement.

The location is FAH 101 and the time for the talk is 7 PM. There’s a reception at 6:30 PM, so getting there early would be a good thing. I plan to be there.